I must confess that I touched Flak Bait when I visited the NASM some years ago.

I hope that it will be assembled and displayed sooner rather than later. I have always liked the Marauder.
As for Carol Jean I think it would be great for it to be displayed as is, not so much to represent a wartime B-25 but a post war "warbird". I would hope that several other warbirds could be retired as is and displayed when the time comes. Let's see what an authentic Mustang looks like next to a warbird Mustang. (Great excuse for a museum to have two of something as well.) The whole warbird and military collectors phenomenon is something that really needs more study from a sociological stand point. I doubt the Romans had Carthaginian re-enactors gathering on weekends, so why is the whole broad experience of militaria collecting such a big part of our culture?
As for different museums approaches to preservation/restoration they ebb and flow and not always in a good way. I remember when I was first interested in warbirds reading about how the USAF museum diassembled an engine (something that was not routinely done as apparently they were treated as solid lumps rather than as machines in thier own right) and was surprised to find corrosion. That led to all the best museums around the world treating their engines to the same restoration/ preservation processes as the airframes. Fast forward 30 years and not long ago some higher up in the NASM was making the point disassembling engines for preservation was a waste of time since their normal oil coating was all that was necessary! Anyone that knows aircraft engines can tell you that inactivity leads to more corrosion than anything else.
The preservation or restoration question is always a complex one but if nothing is ever restored then the skills necessary to do so will become lost; restoration not only brings back the artifact but preserves the skills as well.