I'm trying to think of the technology trees, but I think I would say the doom star might be overpowered.
Yea, iirc it was pretty devastating if one empire got doom stars significantly before the others.
But another way in which things were "imbalanced" there was that by the time you had doom stars, why exactly would you build frigates? Of course, partly this was a mercy: interacting with a frigate took largely the same amount of interface clicks as a doom star. If there were balance reasons where it was to your distinct advantage to produce frigates instead of doomstars, such that you spent the same as your enemy and wound up with 200 frigates vs his 2 doomstars, you'd either just "gimp yourself" by not doing the optimal thing, or drive yourself batty clicking the mouse over and over.
So I guess sometimes obsolescence can be the lesser of the evils
But the "always build everything in your largest hull size" thing crops up in a lot of games in my experience, and it feels like a missed opportunity. Why have all those other choices?
On the other hand, I never quite made peace with SotS system of "sure you could just field dreadnoughts, but the control limit only gives you like 2 of those, vs like 18 enemy small ships". But perhaps it was a step in the right direction. The finite number of ships on the field (regardless of how many was in your fleet) seemed like a good design decision considering the many vagaries of the alternative, but never felt right.