Actually Goa, now that I think about it, I vaguely remember hearing something about allowing for four levels for abilities... That would make a lot of sense and would certainly support what you said. I wish I knew where I'd heard it lol
I also hope that there is some bonus gleaned by sinking that fourth ability point into an ability. Perhaps instead of just getting a set amount more powerful... well.. It's hard to explain... Let's try GRG as an example on a 4 point system according to how I want it...
Level 1: 500 damage -3% mitigation
Level 2: 800 damage -6% mitigation
Level 3: 1100 damage -9% mitigation
Level 4: 1500 damage -12% mitigation -2 Armor
That way you get more of a reward for sinking that last point as it reduces the flexibility of the craft as a whole. And, since they are not going to be appearing in great numbers, you can't just make another one with a different configuration...