I think this is a "have your cake and eat it too" type idea. Having more skill points or raising the level cap would do essentially the same thing.
Having more skill points would just encourage the player to finish out the rest of the non-per-ship skills, further decreasing viable player choice.
You'd have to reduce the global skill points by half to accommodate the change, which then limits what a "global" player is able to do.
Absolutely correct; making this change without adjusting the skill points available to a max level player would be a bad idea. (Although cutting skill points in
half might be overkill. But they'd definitely need to be cut. And some adjustments to the leveling curves might also be a good idea.)
At the moment, a player can acquire all but four of the fleet-wide skills; if we ignore salvaging and surveying skills (which, if we're trying to be efficient, we probably should), then you can get all but two.
If you ignore the industry aptitude entirely (also not unreasonable - the stuff in there is nice, but once you're at end-game and money is no longer a problem, there's no particular reason to run with D-mod ships at all), then you can get
all of the other fleet-wide skills with nine points left over for per-ship (or industry) skills.
In other words, if you aren't inclined to deliberately gimp yourself by overspending on either combat skills or skills that only help in the early game, then we're
already in the situation where "the only meaningful decisions to be made are the order in which you get skills". Which is, as you say, not a good place to be.