Actually the lack of power is the only thing that keeps the Feds from being uber-ships. I couldn't imagine trying to fight against the Feds if they could get close enough to use their photons effectively. As it is, the Feds are over-armed because the G-Racks are simply A-Racks, and the Feds get free AMDs. In SFB, a Federation starship had turn w/o AMD when firing missiles. It would take a serious patch to make the G-Racks work the way they are supposed to. After what happened to the I-torps in SFC EAW's final patch, I would hesitate before letting anyone mod a correction.
Correcting the entire shiplist is an ambitious concept. There are only about 100, maybe a couple less, 2nd Generation X-ships in the entire game. There are well over 2300 lines in the stock shiplist and many, many more in Firesoul's. I think Firesoul's shiplist is the defacto standard. It's much more fun than stock, anyway.
I now have a spare computer and high speed internet access. I've always wanted to run a SFC server. I just wounder how many people would be interested in giving my shiplist a try.
I've created a table for empires and weapon weights to create better balanced X-Ships:
The following is my ideal table for assigning weapons to 2nd Generation Advanced Hvy Cruisers:
EMPIRE Phasers / Hvy Weapons Total
Federation 16 15 31
Gorn 16 15 31
Hydran 16 14 30
ISC 14 16 30
Klingon 14 16 30
Lyran 15 16 31
Mirak 16 14 30
Romulan 17 11 28
General Weapon Weight Table:
Photon 1
hvy photon 2
disruptor 1
hvy dis 2
ph 1 0.75
ph 2 0.5
ph 3 0.25
Ph x 1
ph g 1
ph g2 2
ph a 0.5
ph b 0.5
plas f 1
plas g 1.5
plas s 2
plas r 3.3
plas x 2.5
plas e 2.25
ppd 2
drn a 0.5
drn b 0.75
drn c 1
drn m 1.75
add 6 negligible
add 12 0.25
hb 1.3
fg 1
esg 1.5
Of course some ships need to be fudged ever so slightly to fit these parameters, but this is very similar to the automatic BPV adjustment in Ship Edit. I also make a few minor adjustments to BPV.
By this calculation table, the stock Rom XCA has only 21 weapons, making it miserably under-armed compared to XCA's of other empires. The stock Romulan XCB, however, is pretty close to reasonable with a weight of (rounded to the nearest) 26.
I've wasted a month on this, and reached a finishing point. Well, I guess there's play-testing.

Now, to get my .mct and .scr files in order. I may have to reinstall the game. No telling what all I nerfed up trying to get the EAW campaigns for OP with Nuclear Wessels, and Tracy G's missions. They might have some odious components that I didn't anticipate.