That might be a bit simplistic in design and consequently complicated in practice. If fleets can be regrouped (split up and rejoin in different ways) frequently, then there will be a lot of extra admirals / commanders created, and needing to be dealt with when their fleets are merged.
I think we can alleviate that by eliminating the assumption that a fleet must have a commander / admiral and that it automatically generates its own upon creation. The commander/admiral could be a seperately commissioned item that is then assigned to an already created fleet unit.
The other thing is that an alien race might not even have a system where one person orders another. There form of government might be one which does not allow commanders.
Granted that's a valid point, but I think that just boils down a matter of semantics. Each race could just have a text string in its design template that tells you what to call the admiral-type unit. One race might have "Overlords" and another might have "Consultants" while yet another has "Augers" etc. Since that's pretty open ended, I think a format can be avoided in which an admiral assigned to a fleet necessarily demands that we imagine that individual is in complete control in the same style as human Admiral or Commander.
I think that single command units works better than crew experience for a couple reasons. The first is that reassignable units provides better flexibility, more decisions, than relying on a single starship that "kicks butt". The second is that its a bit more enthralling and while it could echo of micromanagement at times, if the commanders have to be produced / trained with the same kind of effort it make take to build additional ships, one's individual playstyle might lean more towards the simplicity route of just building more ships provided that a command unit isn't staggeringly mighty.
An alternate way to do much the same thing is to have it so that rather than individual units earning experience, your Empire as a whole earns combat experience which can be used to purchase "officers" that each have some ability that they add to the fleet / colony / whatever to which they are assigned. The officers are just nameless clones that can be moved to any place you wish. You might see an interface that looks something like this:
"Available Combat Experience: 221"
"Navigation: Deep Space Expert - 10"
"Navigation: Nebula Expert - 10"
"Navigation: Wormhole Expert - 10"
"Tactical: Beam Weapons Expert - 10"
And so on. That kind of system also emulates a level up system, but with more direct flexibility.