IIRC, the most important reason different crew levels were abolished was to simplify things under the hood, they introduced just too many variables. That's a good reason, but I miss the feeling of having an elite crew aboard my ships.
My idea is: elite crew simply counts as two crew for crew requirement purposes. For crew transport purposes they still count as one. Meaning, you only need half as much elite crew to man a spaceship than you'd need normal crew. That doesn't complicate things very much, does it?
Similarly, you could have unlearned crew that only counts half as much as normal, so you'd need double the headcount. That would also give a reason for transport ships to exist, as ships would need more unlearned crew than they could carry.
I'd also suggest that crew levels are fixed, they don't gain experience. Say, the difference is that some were picked out of the gutter, normal crew went to schools and had some training, and elite crew are from military academies and such. You could only get elite crew in small numbers from military markets and floating cryopods and such.