Suggestion:
Remove the supply generation for engines, and add one point to the hull.
Then you don't have to worry about big ships with lots of engines.
Same with the supply storage points.
And, no I don't have a problem with the generic supplies deal. My quartermasters are psychic, and pick up everything in just the right proportions
I did split up the "energy" supplies and the "matter" supplies in P&N, since that should help diversify weapons research and ship designs.