Mostly because they want to reuse as much of the existing infrastructure at KSC as they can, and it was built around the idea of static buildings & launch pads with mobile launch platforms. When they were building a west coast shuttle launching facility in the 80's, they were reusing SLC-6, a Titan III facility built around having a mobile service tower, so they wound up building a mobile assembly building.
Wait, west coast shuttle facilities, you ask? Yup, they were planing on launching Discovery from Vandenberg Air Force Base in October 1986. Unfortunately, Challenger exploded in January 1986, putting a moratorium on shuttle launches, and it was deemed prohibitively expensive to make all of the safety-related upgrades required once they started flying again, and, at that point, the Air Force had already decided they were better off with unmanned expendable launchers.
Not only that, but when NASA runs out of SMEs for the SLS rocket, they will have to come up with a new engine at huge expense, put it through a testing regime, and more or less redesign the rest of the rocket as a whole new vehicle anyway.
Not quite. Once the stock of RS-25D engines left over from the space shuttle program are used up, they'll be replaced by RS-25Es, a cheaper one-time-use version of the space shuttle main engine. They may need to produce two more sets of the 25Ds before the E's are ready, though. They're reusing the old shuttle engines on a disposable rocket for two reasons: they're already a man-rated design, and the engines themselves are already paid for.
Interesting note, Discovery's engines, at least, may make it to museum some day; looks like they're being earmarked for ground test structures, rather than flight.
...astronauts wearing an ACES, Sokol or some private sector pressure suit...
I sort of hope they use Sokol suits, or something with compatible valves, making it easier for astronauts to go up in one type of space craft and, if necessary, return in a different one. Of course, the seat liners would also have to be compatible with the ones used in Soyuz, but it'd be nice to be able to switch crafts without having to send up a second pressure suite and seat liner, like we did when we had astronauts switching between the shuttle and a Soyuz mid flight.
The main engines and associated plumbing were removed at NASA's behest, not the museums. NASA plans on reusing the them (and, unfortunately, disposing of them) on the first three flights of the new SLS rocket.
I believe they removed most of the tanks and plumbing from the RCS and OMS systems because the fuel they use is particularly nasty (they have to wear heavy-duty hazmat suits when working on them), and they were worried that the equipment would still be contaminated, even after it was purged, and most museums don't toxic self-igniting chemicals in their exhibit halls anyway, so it was safer just to completely remove all the interior components. It's not like they'd be on display anyway, unless you went crawling around in the interior, or the museum did a cut away (which, in this case, just makes me shudder).