I never go on the Midway (even if I hope... one day), but the Intrepid was a nice experience, for the good points there was the visit of the SSG USS Growler, going through the Regulus (then SEAL) hangar, the A-12 Oxcart is a rare piece, F-14D Super Tomcat prototype, one magnificient F3H Demon (the USMC Phantom close to it give you a nice impression of how imposing the Demon was), there is also an old and interesting USCG HH-52 Seaguard, the OV-101 Enterprise is a great add, even if there is (too many?) people which prevents you to taking good shots... many rooms and decks can be visited.
For the bad points. well... like all others museum, we would like there's "special addicted" tickets, with the ability to take pictures of airplanes from everywhere just like a X-serie cameraman and visit all sections of the ship, as being lovers of these wonders we would not break anything.