I never quite understood why they take a percentage in the first place. For non-combat activities that is. It's a bad deal for the commander: the more I make, the more I have to pay them, despite them not doing any more work to earn it than they already were. It's a bad deal for the crew member: when I take time out to material hunting, engineering, or rep/rank grinding -- which makes up a large chunk of my time in game as of late -- they're earning nothing. A flat rate based on their skill level would seem to be the most equitable solution for both sides, even if they're inactive, since what you're really paying for is their time.
Now, for combat activities, the percentage actually makes sense. If you want me to agree to go into a warzone with you, where ships are being destroyed left, right, and center; you're dang right I'm going to be asking for a large share of the booty because of the risk involved. Even if I'm flying escort for a trader, and we're not seeking out combat, I'd still expect to get a percentage of any bounty or "we'll pay you more if you take out these NPCs following you" payouts since that's additional money I've just helped you earn.
So, why not have both? A flat rate (in-game time) that applies no matter what you're doing, and a percentage that applies to any bounties, combat bonds, combat mission payouts (massacre, assassination, take out skimmers, rescue hostages, take out powergrid, steal cargo, etc.), and combat-related follow-on rewards for non-combat missions.