Basic idea: these are three kinds of "cargo". They don't just generically take "crew" space on a ship.
Why: they have totally different requirements. They're going to affect gameplay fundamentally differently. It'll be more immersive.
Sure, they're all humans, but:
1. Colonists are like passengers on an airliner; they brought their luggage and you have to allocate supplies to feed / entertain / bathe / etc.; they cost more than crew in terms of space and other needs. Moreover, they're paying you to move them around; they aren't your disposable redshirts valuable crew personnel. They're totally useless for running a ship, too; they trained in Xenoagrarianism whilst your crew trained in Flux Radiation Flushing.
So they're kind of not equivalent... and the average Hound probably has room for maybe 1-2 of them to hang out in some smelly corner that you've covered in cushioning ripped out of old couches and then put a dozen of those tree-shaped "air freshener" things around to cover up the smell of the last time the 'fresher pipes developed a severe suction problem. Needless to say, you don't make a lot of Credits hauling people around in such conditions; if you want them to be happy, you put them on a Starliner and if you just want them There you put them on a Shuttle.
2. Marines are like Colonists, in that they take up a lot more room and resources than a crew-person. They're less clumsy in space, granted, and they probably know the basics of how Shields work, but they need training spaces to do their pushups, storage areas for their munitions and other material, an armory shop to fix their powered armor, etc., etc., etc. The average ship can transport Marines, but it cannot transport them ready to fight; that takes a more specialized vessel.
So... basically, this would give an in-game point to having those personnel-holding ships around, without making them generic. It'd mean that if you want to deploy a bunch of Marines to raid an orbital factory complex and steal some Blueprints, you'll need to bring along some military transports, for example, because your warships can only carry very small contingents of Marines at most.
Anyhow, this idea would add flavor and give players a genuine reason to want to use those ships that are otherwise entirely useless targets.
Other thoughts about Crew.
1. Other than losing lots of Crew during a fight resulting in a possibly-catastrophic tailspin mechanic happening with CR and maintenance costs... what is the point of Crew now?
When they leveled, they had kind of a point, as an endgame mechanic; I remember people boasting about how they'd managed to spend enough time to have an Elite crew in the thousands necessary to give their lone Onslaught a chance against the Hegemony Defense Fleet. Now, they seem like an atrophied feature; you lose them when Bad Stuff happens, you gain them with money, you pay them in Supplies, you'll never want less than 100% of your requirements, the end.
I mean, Captains largely replaced Crew. They're still not very interesting- they don't talk to you or bicker amongst themselves or send you love letters or say cool stuff in combat, like "et tu, impetus?"... but they're at least fleshed-out as a heroic leveled Thing and they have faces, etc., which is probably enough.
2. Could Crew become interesting? Sure.
A. Crew could be promotable. For example, if you just lost Captain Skippy during a running firefight with the Red Hessians (oops, wrong game) you could figure out which of his subordinates sucks the least, and promote them to Captain. In Iron Mode, this would be neat; Captains could be mortals, but you'd have an answer.
B. Crew as it currently works could go away, and the Captain system could be expanded to include Captains with non-combat buffs and interesting abilities. I won't be at all surprised if we have the ability to appoint Governors of our Outposts; why not have Engineers, who are in charge of fixing up our ships between fights, Scientists who help analyze artifacts or planets we're exploring and Executives who deal with the fleet's business arrangements while in port?
This sounds interesting; instead of having yet-another Supply-like number to chase around, we'd just have Supplies, but in exchange, we'd have something that's actually interesting, with personalities.
"Admiral, we need to pick up more H-Fuel soon, but I've successfully throttled down the Magnetic Decouplers to allow our Burn Drives a little higher efficiency at lower speeds." - i.e., if you have a good Engineer with <insert buff> then you get an ability that kicks in when you're running low on Fuel.
"Your Excellency, I'm fairly certain that if we spend a little more time out of Burn to allow the quantum-crackers to finish their work, we will expose interesting information here." - i.e., you have a Scientist with some ability that gives them a chance to get Domain survey data out of wreckage, etc.
"Sir, we're going to have some trouble with the natives. Nothing we can't handle, but a bit of grease for that 'militia' they use for police might really help get the deal done" - an Executive with <ability> could give the chance to bribe your way out of trouble over using the Black Market, for example.
C. Or, alternatively, make Crew interesting again by giving the player some additional stats to manage. Morale, for starters; a Crew with high Morale fights a little better (say 5% better range, ECM, speed- something minor but useful) or repairs things faster. Maybe Crew need to be rewarded once in awhile to keep Morale up (think: all the special foods in Mount and Blade) and Crew casualties might get offset by high Morale; you can afford to run a little closer to the red line on Crew if you have great Morale (and there's another user for a non-fighting Captain type).
Anyhow, just some thoughts on all this. I'm not sure what Crew's for any more, other than as a bean-counting device; if that's all they are, then why not just keep things to Supplies and Fuel and keep that part of the game design simple?
At least now, when you space the poor little redshirts valuable crew-people, they get put into ostensibly-recoverable cryogenic storage; I no longer feel like Ghengis Khan slaughtering the innocents, lol.