Alex has noted that the skills are not in their final state, need rebalancing/adjusting, and also that when you do hit level 10's part of the design philosophy is that you are supposed to be overpowered in comparison to the AI. (Although if/when AI Admirals have levels that could change...)
With that being said, I think this is a great Idea. I like the thought that your 'combat skills' have a larger impact on smaller crew (Hull? why give extra bonuses to high-tech ships) while your leadership and logistics skills have a larger impact on larger hulls (or more hulls, or more officers...); and your technical skills might be equal across all hull types and sizes.
Alex, while the OP's idea may not be implemented in the next few patches please consider it when you revisit character skills.
But at the same time I hope he make the cap ships much less "hanger queen-y," especially with them being much more rare in the final game. The last thing I want is the cap ships to lose their strengths and become something that is almost worthless.