In my never humble opinion, I think you should try to avoid changing stats too much. For instance, there is no reason to give the alien cruiser a turreted fusion beam. The aliens never used one, so there has to be a reason, most likely due to their organic ships being grown with a hole in the front for the beam, and no way to pivot it, or due to energy constraints from such large shields and such a massive beam. If you don't like it, don't be the aliens. Also realize that that lone cruiser is easy in EV, but if it isn't the last of it's kind, the cruisers would likely hunt in wolfpacks of three or more, and while you may be able to stay behind one of the cruisers, you would get crushed by two other fusion beams lancing your hull.
As a method of balance, simply give the Confeds larger numbers of ships than the aliens get. That is how the story says we won, by pumping out ships faster than they could kill them and then attacking their homeworld.
Of course, I am not playing, so feel free to ignore me, but I think it would be better if you took this under advisement.
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"It is well to remember that the entire universe, with one trifling exception, is composed of others." -- John Andrew Holmes
