Before you read this post I just want to let you know that this is a fantastic mod, if it weren't I wouldn't be wasting the time typing this or playing it. So please keep that in mind as you read on, as the nature of re-balancing means focusing on areas where the game is weaker, and this is meant to improve on an already great thing. It's important to keep that in perspective when someone is pointing out things that they don't think work. Keep in mind that I think most of it DOES work. A lot of these issues are also related to the fact that the AI in Sins is simply not very good, and does not make educated decisions that a human would. In light of this, I've tried to come up with solutions that won't be overpowered in the hands of a human, but that will help where the AI is deficient.
So as I've been playing I've been paying attention to what the AI does well and what it doesn't do so well. A couple random observations. My last few games have been paying most attention to the Romulans and the Dominion as they seem most regularly problematic, so I've been looking at issues they share in common as well as anything else glaring that strikes me.
1) The AI is horrible at using abilities that damage itself. The Romulan Heavy Cruisers and the Dominion Devastator are great examples of this. While thematically I understand the idea of overcharging your weapons, damaging the ship internally, in execution it becomes problematic. The AI triggers these abilities at the sign of any tiny enemy movement. The problem is, they end up going in to important battles heavily damaged a large percentage of the time. It's slightly less problematic for the Romulan heavy cruiser because of re-integration, but still certainly an issue. For the Dominion it's a serious problem, because a human player is really counting on the Devastator's Glory to the Founders buff to make their LR and Heavy ships usable.
A work-around here would be to have these abilities reduce either shield mitigation (or perhaps armor?) instead of dealing hull over time damage. It keeps the flavor of doing something like diverting shield power into weapons, while not causing the AI to do foolish things like send in its Devastators at 40% health (and draining). In fact, if you watch the game play itself out, the AI will rarely keep a Devastator at higher than 70% health, even if it has never even seen a combat situation it had a chance of losing. I've messed around with 6% mitigation loss on romulan heavy cruisers and 5/4/3% on devastators and it results in the ships actually getting in significantly more combat time without the AI accidentally wasting them. Obviously the precise numbers are open to negotiation and further play-testing, but I think the solution is theoretically good.
2) Capital ship problems - Dominion - Taken as a whole, the Dominion capital ships are well designed. There are really only 2 ships that have issues, and even then it is only one ability that needs work on each.
Keldon - As mentioned before, the Keldon needs a replacement ability for its Spiral Phaser ability. Either that or it needs to fire far more often (at proportionally reduced anti-matter cost) and for more damage. Against a standard Federation ship with 50% shield mitigation, and 40 armor, a 400 point blast is really only doing about 66.6 hull damage. Even if it were firing every 10 seconds instead of every 30 it still wouldn't be worth justifying the loss of a point in either of the other two skills. I wish I had an easy solution for you here, but as it is the AI takes this ability a fair percentage of the time and effectively nerfs themselves. At this point I've just got it firing twice as fast for twice as much damage as it currently does, and it still doesn't feel overpowered.
As a complete side-note, I mentioned in my first ever post on these forums that I personally resized this ship about 50% larger, upped its hull and shield values, slightly upped its DPS and bumped its cost up to compensate proportionally. I know it isn't canon and you guys are pretty into that, but the ship felt fairly out of place being almost the exact same size as a Galor. Visually during battle it is also virtually indistinguishable. Half the fun of this mod to me is turning off the UI and watching the big battles unfold, so I like to see the Keldon more easily. This is all very nit-picky I know, but I'm only mentioning it because I am pleased with my results. It's still no match for a Galaxy, but it stands out amongst the Cardassian ships as the obvious "I'm the Cardassian flagship" ship.
Harbinger - Divert power to engines. While a fine ability, realistically this is the least useful ability on the list. The Harbinger itself stands out as the lone Dominion ship to not buff the fleet in some way, and this is fine. But having it rush at high speeds headlong into the enemy fleet and being destroyed before everyone else gets there can be an issue (in the hands of the AI, that is. A Human player would send in Cardassian ships, followed by caps, followed by Jem Hadar. The AI is dumb). At the moment I have it replaced with a fairly weak +shield+hull regen ability (caps at +30/15), which is super uninventive but does sort of promote its status as a powerful battle-cruiser. It ends up playing more like a Galaxy class than anything this way. There are a number of options other than a shield/hull regen ability, obviously. It's just that the really high speed thing ends up hurting it more often than helping it in the hands of the AI.
3) Capital ship - Romulans: ugh. This is kind of a painful one. The truth is, the D'derix (forgive my spelling if that's wrong) is the only one worth building. It is awesome. And powerful. And the only viable way to spend your command points. I promise I will get back to you on this with ideas of how to make each Romulan Cap ship bring something unique and powerful to the table, but right now they need a major re-assessment. But the awesome self-buff (Praetor's talon i think?) and the summon make this the only capital ship i want to build. I don't exaggerate when I say that I would rather have 1 of these than 2 of any other Romulan capital ship. Anyways, let me get back to you on this one.
4) Federation Nova, study shields. -100% shield mitigation is basically an auto-kill on any non-borg ship (as mitigation continues reducing incoming damage even once shields are down). And it lasts 30 seconds!! And it comes off a cheap ship! The AI is decent at using this ability, which is moderately terrifying, but a Human would abuse this to kill every one of your capital ships in the first 20 seconds of battle. I changed it to -20% (nerfed by a factor of 5) and I'm still afraid it might be OP.
The Sabre also needs some serious love. The tractor beam repulsor just doesn't do much 90% of the time (maybe add some straight up hull damage to it?), and the shield-share ability shouldn't disable its target. No fun seeing a level 7 Sovereign sitting there disabled for 30 seconds while a Federation fleet is smashed because its own support ship took it's primary damage dealer out of the important part of the battle. Same goes for the Romulan Black Wing. It's shield regen ability still isn't OP if it doesn't disable its target. I've tried it, it's much less problematic all around without the disable.
The next two things I am going to look at in depth are the support ships and their varying degrees of usefulness, and the Romulan capital ship rehabilitation program. Hopefully some of this is useful to you guys!