All factions have slight weaknesses / strengths at points in the game.
Sera have issues with early raiding capabilities.
UEF tech 3 land sucks until you progress into t4 where percies become useful.
UEF don't have a real answer against subs (Their destroyer torpedo dmg is awful and the torp boat blows)
UEF TMD is horrendous against cybran TML (I'm not sure if its a bug or not, but it takes like 4 TMD to stop a single missle sometimes)
Sera T2 navy leaves alot to be desired in naval combat (Their cruiser is quite good tho)
All faction ACU Hp can affect early outcomes of battles (Cybran needs to be careful, UEF can trade shots etc etc)
UEF bomber is horrendous compared to other factions.
(this is just what i could think of, with a bias towards playing alot of UEF)
Instead of trying to balance every little issue that separates the factions, I'm interested in looking at trying to make them more unique. I think it would be great to add more faction specific units, similar to how the T2 Bots were added to vanilla. Another option is to make the ACU upgrades more unique. Those are changes that would really add to the game in my opinion.