Seeing how a lot of things with AIPs have been resolved, I want to discuss weapons/defenses one last time.
This is why I think weapons are imbalanced, it's a long post, so bare with me 
All weapon tiers in CU except 1&2:
Cost - 1,0 : ~1,25 : ~1,45 ratio (Mass Driver, Missile, Beam)
Maximum possible damage - all are equal, with only Missiles being more effective on larger hulls (10-15% more damage on average).
Research costs: negligible difference (28k vs 33 vs 30).
If we exclude first tier of weapons, which is extreme and weapons don't follow any rule, and tier 2, which is the only semi-balanced tier in a whole tree (especially past Small hulls), weapons allow you to outfit ships with about same amount of damage. Examples:
Small hull, 0% miniaturization, tier 2 (excluded as is quite balanced):
- Particle Beam II: 6 damage total, cost - 175 bc total
- Harpoon II: 6 damage total, cost - 160 bc total
- Singularity Driver II: 4 damage total, cost - 100 bc total
Medium hull, 10% miniaturization, tier 3:
- Plasma II: 15 damage total, 355 bc
- Photonic Torpedo II: 20 damage, 360 bc
- Pulse Cannon II: 16 damage, 240 bc
Large with 30% miniaturization, tier 4:
- Phasors III: 65 damage, 1005 bc
- Photon Torpedo III: 72 damage, 880 bc
- Graviton Driver III: 60 damage, 660 bc
Huge with 45% miniaturization, tier 5:
- Disruptor III: 147 damage, 1895 bc
- Anti-Matter Torpedo III: 176 damage, 1760 bc
- Quantum Driver III: 162 damage, 1400 bc
Huge with 60% miniaturization, tier 6:
- Doom Ray: 288 damage, 3080 bc
- Nightmare Torpedo: 360 damage, 3050 bc
- Black Hole Generator: 300 damage, 2320 bc
As you can see, past tier 2, every weapon can max out at the same or very similar damage value, with the only difference between them being the price for a ship. Beams are 40-55% more expensive then Drivers, and are also weaker on several occasions. There are no differences, they do not introduce any fun mechanics, and boil down to picking strong, average or weak option (Mass Effect anyone?), unless you play on slowest tech speed (if you do play on slowest tech speed exclusively you can ignore this post, as you probably never reach weapon tier 3 or 4 frequently enough to care for any of this). Therefore choosing Beams is just like voluntarily picking -% military production. Problem of weak Beams is magnified even more, as shields are best at increasing defense, so already expensive and only average Beams are easiest to counter.
You may argue that all this brings more randomness and challenge to the game. There are a couple of issues with that, and here are main arguments against current weapons/defenses progression:
1. You hurt players who do not know about this. If they pick Beams their fleets will have almost same damage as if they picked Missiles of Drivers, but will have 30-50% less ships then Driver users and 10-20% less ships then Missile users, who's weapons are also 5-20% stronger.
2. You do not make game more challenging. On the contrary, if the strongest civ in galaxy picks Beams and loses to you when you pick Mass Drivers/Missiles, it feels more like cheating then outsmarting the AI. AI is hurting itself without even knowing it.
3. In vanilla, Beams are the best pick of any weapons. This is thanks to OP Disruptors, Phasors giving you quick access to Doom Ray and Beams being overall cheaper to research then Mass Drivers. In other words, current progression is against original design, which made perfect sense: beams cause damage almost instantly, their accuracy is higher then Mass Drivers and Missiles which can both miss a lot more, and in all Space Operas/Dramas/Movies shields and beams are primary weapons. They ought to be strongest. Mass Drivers used to be weakest, now they are a better choice then Beams, why? Only Missiles stayed more or less in same position.
4. Some tiers of defenses/weapons had different number of levels. Now everything has 3 levels. This makes the tree less interesting, especially defenses - some had 2 levels, some had additional tech in its tier (like Superior Duranthium etc.)... one tier of defenses got cut out completely (Invulnerability Field techs) for no reason, and tech costs/defense values for other shield techs got raised to artificially compensate - again, why?
5. Lost production even in case of cheapest ships is almost non-existent if the average amount of time to build a ship for the AI is anywhere from 10 to 40 turns.
6. Level 3 of lower tiers happens to be stronger then level 1 of higher tiers a lot, this was the case in vanilla on couple of occasions, but on a much smaller scale. Examples:
Particle Beam 3 > Plasma 1
Phasors 3 > Disruptors 1
Pulse Cannon 3 >= Graviton 1 (small difference in price, Pulse Cannon being more effective on small and medium hulls)
Graviton 3 >= Quantum 1 (same as above)
Stinger 3 > Harpoon 1 (on small and medium hulls with 0-10% miniaturization).
Sparrow being better then Stinger I on small hulls if miniaturization is lower then 20%.
Maser being better then Laser I and Kinetic Stream I on small hulls if miniaturization is lower then 20%.
And probably some others I missed.
This is a problem for the AI who upgrades its ships a lot - it pays enormous amounts of bcs for ships that can end up being weaker then what it already has.
Other stuff that goes against original design:
Ion Cannons - were much smaller then Railguns - and even slightly smaller then Lasers. Not only their size when compared to Railguns, but also size mod had lower value.
Kinetic Streams - while still overpriced a little, they were even smaller in vanilla, and this was the only reason why they were expensive - ships with KS3 were almost as strong as tier 2 level 2 (Particle Beam 2).
Seeker Missiles - used to be stronger then Stingers, not weaker.
Ion Beams - were larger then Plasma.
Gaunathor had a good idea when rebalancing weapons. Unfortunately he did it the wrong way - instead of lowering damage of beams and keeping the cost, damage should be left alone and costs raised.
I made a spreadsheet with comparison of the weapons and defenses, in which I also made a separate sheet to make my own changes to fix some of those issues - note that this is a preview and consider it still work in progress (I'm working away this week so I don't have much time to play or test things). After I finish with weapons, which needs a bit of polish, I want to give defenses a go and balance them out as well.
The changes I made so far:
- Fixed most weapons being weaker then their preceding tiers. Some values of max damage had to be increased. Some size mods and size values were changed - for example, made starting weapons bigger and equally bad. In case of Harpoon I and Photonic Torpedoes I, they are not weaker anymore, but dish out about the same damage. They are cheaper as you research the following techs (II and III), so cost is not static within those tiers. Not pretty but does the job done and doesn't make next techs any less important.
- Beams are 20-30% stronger then ships outfitted with Mass Drivers. 40-60% more expensive as counterbalance. A move closer to vanilla.
- Changes to missiles to scale better on higher hulls - lower average damage then beams and comparable with Mass drivers, but scale better on large and huge hulls - in other words, they work better with bigger hulls then miniaturization alone. Goes well with original design.
- Made Kinetic Streams and Seeker Missiles smaller (so ships end up stronger) like they are supposed to be, just as in vanilla.
- Made Ion Cannons a bit smaller, same as above.
- Ion Beams are bigger, but still better then Plasma. They also scale better on larger hulls, like in vanilla. They were hardest to get right (being bigger/better) without redoing the whole tree, so I went the ugly way (like in vanilla), and made 3rd level with higher damage and price.
- Remade Evil weapons. My concern is that AI may be picking weapon modules with highest damage value when designing ships, so it might be possible that even as the AI reaches 4th tier of weapons, it still might use Evil weapons, as they are just copy pasted with changed price and all other stats the same. I made Evil weapons slightly better in terms of damage, but also made them worse at scaling on larger hulls.
https://www.dropbox.com/s/q6bhw92ysb6ivom/Weapons%20reworked.ods?dl=0
This is the spreadsheet I made, I hope everything is easy to read and compare. I left miniaturization values in vanilla sheets unchanged from CU, as it is not that important.
In general:
Ships with Beams will be strongest early, but will be costly. Every 10% increase in damage will mean 20% increase in cost over comparable damage of Mass Driver ships, 20% in 40% and so on.
Ships with Drivers will be weakest, but cheapest and fastest to produce.
Ships with Missiles will be more or less on same level as drivers, until bigger hulls are available - higher tiers of missiles will be even stronger then Beams on Large/Huge hulls. They might be pricey on smaller and medium hulls, but overall they are cheaper then Beams in damage/cost.
If you are ok with those changes I'll edit the GC2Types.xml and start working on the defenses.