My memory does strange things sometimes, but I think I remember even Ironclad people mentioning that they disliked the way that capital ships inevitably gain all their abilities, rather than specializing in one or two fields. I believe it was mentioned that the cap ship ability system would ideally be more like starbase upgrade modules - you make the ship with a specific purpose in mind, whether it's armor, weapons, fighters, trade, etc.
Besides this, there are some cap ship abilities that I would (generally) prefer not to use. For instance, the flak ability on Kol battleships - IMHO it eats up too much antimatter, and I would much rather have the shield enhancement or a high-level gauss shot. Yes, I realize I can just disable it, and I generally do. (Someone's about to argue and tell me flak is awesome, I can feel it. It's just an example folks.)
My suggestion is like this: instead of forcing the player to pick a specific upgrade, they also always have the option of just increasing hull points by a certain percentage, maybe for a maximum of two or three levels. I would gladly take a 10% HP boost over Missile Turret or Embargo in the late game.
This would also (somewhat) alleviate the problem of capital ships being mass-targetted. If you wanted to be really ambitious you could offer a generic weapon upgrade and armor upgrade as well... you know,
"flux capacitor - increases all weapon damage by 10%"
"endgame - totally ripoff the batmobile, increase armor by 5"
"shielded thermal exhaust ports - reduces vulnerability to weapons fire, with a net 10% increase in survivability"
"double decker docking derricks - increase fighter capacity by 1 squad"
What do you think?
EDIT:
To summarize my revised idea below, there would be just one "generic" upgrade per ship. It gives regular bonuses IN ADDITION to what you automatically get for a ship leveling up. So if you get 50 extra HP for a ship leveling up, this is in addition to that. But it is a REPLACEMENT for an ability or extra level for an ability. You click this instead of clicking "Embargo, Level 1" for instance. It would give an upgrade to the ship's HP and Shields, but also one unique upgrade for each class of capital ship. What I mean is, a battleship might get extra amour, while a carrier would get extra strike craft capacity.
For a working example, you might have the following ship. All upgrade stats are completely made-up, I don't have them memorized. The ship in question is based on the Sova Carrier.
Level 1: It's the late-game, I don't need Embargo or Missile Battery, so I get "Heavy Strike Craft".
Level 2: For achieving level 2, I get +5% HP automatically. The second level of "Heavy Strike Craft" is not yet available, so I can either get Embargo or Missile Battery, both of which are useless in the late game. But instead, a new ability has opened up next to the "Train new level" button, called "Systems Upgrade" (or something). It will provide me with things of practical benefit at this stage in the game: +4% HP, +4% Shield, and an extra wing of strike craft. I choose the Systems Upgrade rather than the basically useless (at this stage of the game) Embargo or Missile Battery.
Level 3: For achieving level 3, I get +5% HP and an extra wing of strike craft automatically. My carrier now has 5% + 5% +4% HP, +4% Shield, and 2+1+1 Strike Craft capacity. The second level of Heavy Strike Craft is now available, so I select it.
Level 4: For achieving level 4, I get +5% HP automatically. The next level of Heavy Strike Craft is not yet available, and the Sova's "special" ability hasn't been unlocked yet (Armistice? I forget what it is. Anyway...). So I get another level of Systems Upgrade. For this level, I get +5% HP, +5% Shield, +1 Strike Craft Capacity.
Level 5: For achieving level 5, I get +5% HP and yet another wing of strike craft automatically. The next level of Heavy Strike Craft still hasn't been unlocked. I get another generic Systems Upgrade instead, netting me an additional +6% HP, +6% and ANOTHER wnig of strike craft. This thing's really turning into a carrier! For a summary, so far I have: +20% HP from leveling, +15% HP from Systems Upgrade, +15% Shield from Systems Upgrade, and a total of 7 wings of Strike Craft (2 to start, 2 from leveling, and 3 from Systems Upgrades).
Level 6: For achieving level 6, I get +5% HP automatically. The next level of Heavy Strike Craft is available! I choose you, Heavy Strike Craft L3!
Level 7: For achieving level 7, I get +5% HP automatically and still another wing of Strike Craft. The Carrier's super-special ability has just been unlocked (whatever it is... pretty sure it's not armistice, but it's one of those). I feel compelled to choose it, for the button is such a pretty shade of blue.
Level 8: For achieving level 8, I get +5% HP automatically. There are no further ability upgrades I'm interested in, so Systems Upgrade it is. +7% HP, +7% HP, +1 Strike Craft.
Level 9: For achieving level 9, I get +5% HP automatically. AND MROE STRIK CRAFTZ! No abilities I want. I grab the fifth and final level of Systems Upgrade. It gives me +8% HP, +8+ Shields, and... OMGWTFBBBQPOW 2 extra wings of strike craft! It's like an ocean, only instead of water, strike craft! There's strike craft everywhere! This thing's a real frakking carrier!
Level 10: For achieving level 10, I get +10% HP automatically. And.... nothing else. Sorry. Yikes, no more levels of Systems Upgrade available either. Errrr... I guess... I'll get Missile Battery...? Well it's... it'll be one more gun I guess. Still, I feel full of confidence in my Capital Carrier, for all of my automatic upgrades from leveling and the further upgrades from Systems Upgrade have given me, in total:
Base Stats: 2 wings of Strike Craft.
From Leveling (Automatically received): +50% HP! (EXAMPLE statistic) Leveling also got me 4 wings of SC and L3 Heavy Strike Craft.
From Systems Upgrades: +30% HP, +30% Shields, and 6 wings of Strike Craft a'swarming.
In total: +80% HP, +30% Shields, 12 wings of Strike Craft.
Again, the automatic +5% per level HP bonus isn't something I'm suggesting, it was just a completely arbitrary figure to ensure people understand that the "Systems Upgrades" are in addition to standard per-level upgrades.