Feds ARE the good guys after all...
just kidding.
The game is not built to balance each individual ship against one another. (Though some of the excellent mods have made efforts to do so) If you can't get the Sovereign using one ship, call up a buddy and bomb it with two...
There is no doubt in my mind that Quantums are the best weapons in the game, but they are also expensive and heavy, So if you can't win tactically, win strategitcally by choosing some creative builds for your ship(s).
But that's not my point. I'm not a very godo SFC3 player either... I'm sure there are better advices abound.
My point is, it's not true that there is "just now a _beta_ patch for it".
This is the Second (or third depends how close one monitors the game) beta patch
.