Lack of qualified operators is real operational problem.

Majoring in physics pretty much guaranteed you a NROTC scholarship, if you wanted one, back when I was in undergrad. Around a third of my cohort (and the ones graduating immediately before and after mine) were in NROTC, and every last one of them was earmarked for the nuclear program when they finished school.

I'd speculate that the Navy simply doesn't have enough personnel to put a nuclear drive-train on every cruiser, much less the entire fleet.

Edit: grammar

Edit2: Also, keep in mind that aircraft don't run on uranium. A carrier group needs tanker replenishment anyway, so switching to nuclear ship propulsion doesn't save you from needing to worry about the logistics of transporting large volumes of flammable liquid to the group.