Another interesting read, Alex. One thing I noticed is that you're very concerned about "gameing" the system. Exploiting the mechanics in an artificial way. This is a very good philosophy regarding game mechanics. But, I have one concern:
Is it going to be possible to use hit-and-run tactics with a smaller fleet to grind down a large opposing fleet? This is something I was very much looking forward to when strategic aspects like this came into play, but from what I'm seeing this might not be at all possible or feasible.
Eventually, if played carefully, a smaller fleet should be able to carefully whittle down an opposing fleet, but it shouldn't have to be ship-by-ship. Maybe CR should be deducted according to damage taken (or is this already the case?)
Fun question

For a smaller fleet trying to whittle down a large one, I think the most viable way would be indirect, by disrupting its lines of supply - supposing that's an option and the large fleet isn't operating in home territory within easy reach of friendly bases.
There is some CR deduction for having weapons/engines disabled in combat (applied afterwards), so that could be a way to do what you're describing. Really, though, if you're at a point where you're dealing significant enough damage to achieve that, you're probably also at a point where you could take down the whole ship.
On the whole, being able to grind down a fleet without facing its ships in battle is something to be very careful of. If the design allows that, then it might also allow bypassing battle altogether if whatever strategies explicitly allow for that are taken far enough. If they're longer term and take time to play out in the campaign, that's one thing. If they consist of just carefully selecting options in the encounter dialog, that's another thing entirely.
I've also got some vague ideas about encounter options (perhaps unlocked by skills) that would allow a smaller fleet to isolate a portion of a larger one to fight against. It's not something I want to start out with, though, but something I'm going to keep in mind in case the campaign shapes up in a way that makes adding something like that desirable.