There are some big issues with what you've suggested:

1) It's extraordinarily complex, so it's going to take a lot of development time away from other features.

2) It's management intensive

3) This makes starbase choke points way too powerful, essentially preventing bypass tactics that are critical to breaking stalemates

4) There's really no reason to punish people for making "deep raids".  With starbases on the scene, the balance is pretty good in that respect and weakening this tactic would probably be counter-productive.

I don't think it has to be complex at all.

It worked well in conquest frontier wars, which had a very similar multi-system layout. People still love that game.

What it would mean is that a deep raid might see you tell your fleet not to fire as it passes through systems. At the moment fleets have an "american in vietnam" style attitude... fire as much as you want. More ammo is coming. 
Especially when we can make beam\power recharge based weapons less powerfull but more handy than kinetic based weapons just by  giving them ammo counts.

Personally Darvin3 I hear what you are saying and where you are coming from. But think it could work.

nay sayer

Whiskey I understand what you are saying. Some good ideas there.

I have not really thought of antimatter as supply before simply because ships do not stop moving or firing because of it.

The other thing that would be nice here is if as part of supply new capital ships actually had to be researched and in some cases existing ones in service with your fleet could be dry-docked for conversion.

The dry-docking part would be neat. However, I don't think we'll see it considering engine limitations.

Personally, the kind of dry-docking options I'd like to see would be docking a frigate or capitalship with a capital ship or starbase, respectively, for repair/resupply. Or general transport. That last one is something I'd love to see.

Happens to us all. Though I think it's funny that I understood what you were saying even if you didn't say it all the way.

Fighters do dock before transport. And I personally would like this because it would be mega-cool.

Gameplay wise, here's some effects I've thought of:

1) You could use it to "sneak attack" an enemy; while the enemy does know you're coming (if they've got phase lane monitoring techs done), they can never be certain just how many ships you're bringing to the party.

2) You could introduce system defence ships, where a ship is basically phase drive-less; these ships could be more heavily armed, armored, and shielded, but be much slower than a phase drive equipped warship. If you need to redeploy them, loading them into a big transport ship would be perfect.

3) It would fit with the theme of the new ship class introduced, corvettes. Corvettes are supposed to be smaller than frigates, IIRC, and if a corvette required a large transport to dock with to easily and quickly deploy throughout a map, then that would add tactical and strategic depth. Fluff-wise, a corvette might be large enough to mount ship-grade armor, reactors, engines, and weapons, and even carry shield generators, but not large enough to be capable of mounting a phase drive.

4) It could probably fit with the theme of either the TEC or the Vasari; in the case of the TEC, it's a big repurposed vessel designated for bulk warship transport. For the Vasari, it's a way of ensuring that no ship get's left behind while they're on the run from whatever they're running from.

Transporting corvettes and building frigates and cruisers might be a purpose of the Titans, that is a major reason for building something on that scale.

You can create a ship ability/buff for each type you want that depletes 'x" amount of antimatter per minute (or change the values on the ship entity files for how fast it recharges. You could adjust these values until you were happy with the outcome and even reduce all the recharge rates to zero. Some ships would have to have antimatter costs and capacity added to them and their weapons types.

You can then modify any existing facility, ship or ship ability or create new ones that charge friendly antimatter at a certain rate--these would be your refueling stations and tankers.

There are already buffs that effect antimatter and if you study how to mod you could learn to use them. Balancing would be the part that took some real thinking on.

As to ammunition itself, there is no "ammunition" buff though I believe there is an ability that increases the rate of fire. You could possibly create an ability that had a trigger for the refire rate dropping to zero but I don't think it could be easily done and it wouldn't be based on shots fired but would rather have to be something like hull damage or antimatter levels as a whole.

And you might want to hold off a major rewrite of the game until rebellion is out

Anything is doable in some way if you are creative and accept some compromise--practical--that's another story. I like the concept of the Z-axis ship mod that allows you more up and down motion but it has deleterious effects as well--the AI gets pretty confused with it sometimes and it alters planetary defense capability. Still it's a great proof of concept and worth trying

It's actually an interesting idea but it would change a lot of dynamics of the game but more importantly would really mess with the AI...which might not be able to cope with the changes and that's probably what will castrate these suggestions as workable (and they would require a bit of work).

Off the top of my head, using antimatter as a trigger you could pretty easily make a ship stop moving, stop hull and/or shield repairing, disable its abilities, stop it from jumping and stop it from firing.

Kitkun's suggestion is simple and elegant, I like it.

Also, culture bonuses can sort of stand in for supply since your fleet can get different bonuses like AM (TEC), shield mitigation (Advent), and weapon damage (Vasari) and it requires your fleet to be near your own planets. Perhaps a broadcast center can double as a supply depot?  I've made some raids into enemy territory and noticed my AM wasn't regenerating as fast as usual (as TEC). Who says the factions' culture aren't different from each other?

Perhaps new research could be added for more faction-specific culture bonuses.  How about shield regeneration for Advent, Hull repair for Vasari, and ROF for TEC (you could make a case for flip-flopping TEC and Vasari bonuses but here's my reasoning.  TEC "normal" ROF is the crew being selective about their targeting but the bonus gives them more ammo to play with, while the Vasari need to last longer deep in enemy space to do more hit-and-run attacks).

Of course, a good case could also be made for all factions getting these culture bonuses b/c power plants need fuel and hulls (and solid ammo) need raw materials.  Obviously some structures do this but this so there would be some redundancy but this would probably come into play more when attacking a neighboring system (cf. Advent's AM recharger with TEC's culture bonus).

Also, maybe the rebel factions could get different culture bonuses in Rebellion.

You could probably do some of this with a mod or at least bump up the existing bonuses with one.  (Might be something to try, actually).

If I've made any factual errors about existing game mechanics, let me down gently.

You will be disappointed when someone like me defeats you with a frigate centric strategy.

It seems sir that you fail to understand the premise of supply lines and supply ships.

Take enough supply ships, either protect them in a nearby friendly or neutral system, or take them with you.

If your not behind enemy lines you will be supplied by supply ships that flow along the trade lanes.

If you do not do this then yes you will run out of ammo.... the whole history of warfare is about supply lines. Generally those cut off from supply LOST! You get surrounded "you lose"! You raid to deep without enough supply and support "you lose"! Your empire does not have enough raw materials for ammunition "you lose"... historically some armies were better trained and equipped than their adversaries... but the enemy had more shere industrial and resource might. The better trained and equipped army won all its battles and then LOST the war. 

In space I imagine that "hidden" supply bases would play a huge role. The history of warfare again is in part about ships re-supplying back at base or at a neutral port and heading out undetected again.

In short if we ignore supply lines then we assume each ship has generations of families and is self sustained in both energy and raw materials. In short each ship is its own world.

For one, maybe he just thinks that it wouldn't, say, add anything fun to the game.

However, your premise of supply lines is simply stupid. First off, yes, the history of warfare has, and will likely, played an important part in the likely continued future of large-scale conflicts.

Unfortunately, space warfare is drastically different from anything that has ever been done before. First off, just how do you propose to hide these supply bases, and keep your ships undetected? Because if you think that's actually possible, you have no concept of just what space is really like.

Space is dark, and cold, yes. Which is exactly the reason why it's a terrible place to hide. Because it's so dark and cold, it means that any ship operating at normal capabilities (i.e., keeping the crew from freezing/cooking to death, keeping the ship from crashing into some random planet, whatever) will be visible for a very long distance.

You due a maneuvering burn, you get spotted. Keep in mind that the Space Shuttle's main engines can be seen from very far away. As in, from beyond the orbit of Pluto far away. A ship in the asteroid belt could spot the Space Shuttle's maneuvering engines. And a puny ion drive puttering away at one one-thousandth of a gee could be seen from a distance equal to the average distance between the Earth and the Sun.

And really, "self-sustained" in energy isn't too hard. You need to burn very little nuclear fuel for a gigawatt of power, and a gigawatt is, on average, similar to what the usual nuclear plant produces, for many, many homes. And that's on fusion power. In fact, assuming I've done my math right, a deuterium-tritium fusion reactor with a 95% efficiency and producing 250 gigawatts requires a little less than 6,000 kilograms of nuclear fuel. For around sixty years of continuous operation.

Furthermore, it's not a stretch to think that these ships would be heavily automated, reducing crew requirements (actually, a realistic space warship would likely be entirely robotic. Cheaper that way.). A spaceship really is it's own little world, though you've made an enormous leap in logic going from "no supply lines" to "generations of families and self-sustained in energy/raw materials".

Additionally, space, being a 3D environment, more or less has no boundaries. It's nigh impossible to blockade a planet. A space station, sure, you could blockade that.

A station in orbit of a planet, not so much. Because that planet can have much bigger and more deadly guns than your spaceship ever could.

It's also not unreasonable to think that these ships are equipped with a small manufacturing facility (or at least the larger ones) to assemble replacement parts or machine new ones as needed.

I wonder, though, did you ever read or hear about the SpecOps units that helped to liberate Afghanistan from the Taliban? Because those guys were dropped deep in enemy territory with little to no logistics support. Sure, they probably got the occassional supply drop from across the border, but most of their supplies probably had to, *gasp*, be secured from local resources.

Probably the biggest thing you've ignored, however, is the fact that supply lines may very well be implemented in an extremely abstract way, or, *shock*, the devs didn't think it would be a fun mechanic. No matter what you say, if the devs don't think it would be fun, then it isn't going in.

Except, of course, space warfare will be completely unrelated to the First Punic War. Or in any way resemble, the First Punic War.

It also doesn't help that Rome more-or-less had other advantages, like defending home turf, familiarity with the terrain, familiarity with the weather, not loosing a bunch of guys from going over some mountain pass, etc. etc.

I'm not saying I know what space warfare will be like, and I wasn't saying that space-borne warships would operate like specops units in Afghanistan.

I was using that to point out that you do not need supply lines on an interplanetary scale. This is because once you're going somewhere, everyone sees where you are going, and can figure out how long it will take you to get there.

It's simple thermodynamics, trigonometry, and physics. At it's most basic, figuring out those details will be mathematics.

As for the idea that every ship carries minimal crew, there's really no way to gauge what is "minimal" for a warship in SoaSE. We have no idea how big these ships really are, no idea what their performance and destructive firepower is. More or less, there's no way to frame the ships in Sins against a real-life unit system, like watts, joules, and Newtons.

Note that the manual does give crew sizes, and that in the case of the Vasari said ships have very large crews. However, the Vasari's case is easily explainable: their entire species is on this fleet. Of course their ships are going to be packed to the gunnels with individuals.

However, space combat simply couldn't look like the Punic Wars, for the simple reason that space is a fundamentally different environment. For example, you can't really get an "encirclement" in space, because the enemy can go above or below the circle.

An "englobement", would be harder; you'd need either numerical superiority or for warships to be close enough together that they can easily be surrounded. Ships are also a lot different than an individual; in a big war, people will die, and ships will be lost. That's what happens.

But the monetary cost of training&equipping a Punic War soldier, as considered in modern terms (accounting for inflation and depreciation) will be vastly less than building even a rudimentary, fully autonomous warship.

This monetary cost is all relative when it comes to a galactic empire vs the roman empire.