Another idea I've heard before is rather than cap the number of skills, reduce the effectiveness for subsequent ones. For instance, something like skills 1-3 operate at 100%. Skill 4 85% skill 5 72% (example numbers), and so on, so that while you can always gain more skills, subsequent ones are less effectiveness. In this case a 4th skill BOA would grant a 4.25% bonus to crew. Tie this in with reworking bad perks and skills, adding a few more to some crew members, and lessening the exponential experience cost of subsequent skills.