@OP
The problem is the long term effects of powercreep.
Sure, it may start by making things a bit stronger, battles ending a bit sooner and all but over time this mentality stacks up and battles keep speeding up more and more, ships will be tearing through shields faster, instantly killing other ships all the time, and the game turns into a show of ships exploding everywhere instantly with little to no counterplay involved.
Just nerfing everything has the problem you mentioned, everything ends up turning into a clunky, slow ship that feels like it's dealing no damage.
There needs to be a balance, if a few ships are sticking out they are probably overtuned, if a few are just bad and nobody picks them they should be brought up instead, and if it's something making an entire category of ships OP (say, phase) then that system itself is probably what needs to be addressed.
(That being said the Doom problem goes further than just the phase issue)
Also, as I mentioned before, with the introduction of story points the game will have to make a choice, what will it be balanced around?
No built in hullmods? Then when you start doing it the game will lose all challenge and everything you field will be OP
1 built in hullmod? Then you'll still be OP by placing 2
2? Then you'll be crap untill you start adding them, and when you finally spend millions of XP by placing 2 hullmods on every ship you'll finally achieve the state of normality which you used to have by default before this sytem was implemented, and when you get 3 you'll be OP anyway (worst balance, probably)
3? Well now everyone who's not at late, late, late game, using one specific skill will be underpowered, and when you finally get there you'll just get even.
I'm not looking forward to how this challenge will be solved by the devs. Sounds like a ton of work, perhaps impossible.