Houston doesn't exactly treat thier artifacts with much respect either, just look at the state of thier Saturn 5 compared to KSC's or Marshall's.
If you ask me Enterprise should of gone to the USAF Museum as orignally planned
I would have liked that very much.
My favorite place (see avatar)
NMUSAF is the #2 aviation museum in the US in terms of collection after the Smithsonian, and they would have been VERY qualified to look after her. (Probably #2 in the world, are there any others out there with more than 360 aircraft?) They include in their collection already a shuttle payload (DSP), and an intended payload (hexagon), a Titan IV launch vehicle, an original X-15, etc. They would have keep Enterprise in a climate controlled building from day 1. Oh yeah, and you would not have had to pay one cent of admission to see it.
I don't know why that they weren't chosen, but I presume it was because they were expecting more people would see it in New York. Dayton, Ohio isn't as "sexy" a city as LA, New York, Orlando, or Washington D.C. I don't know what Intrepid's yearly attendance is, but NMUSAF's 1.3 million is at least on par with the California Science Center. Or, NASA didn't want to emphasize the military application of the shuttle which would have been the case had it gone to a military museum (which I kind of get). Intrepid, after all, is still a private venture.
Still, Dayton got a crew compartment trainer, which is cool. You'll be able to see the flight deck up close, and they are planing an interactive exhibit around the thing. So, overall, I can't complain.