After thinking about it and sleeping on it, here's basically where I stand.
1. Preserve the exterior.
2. If the queue must change, keep it in a sleek "retro-future" style that still evokes a '70s flavor; keeping the queue music loops is absolutely non-negotiable. Dark, half-eerie/half-calming ambiance is essential.
3. If the exit must change, try to keep the show scenes (or equivalent scenes); it's such a nice little touch that not only further distinguishes Magic Kingdom's Space Mountain, but they also act as a tribute to Walt's ideas of futurism and space travel that are foundational to Tomorrowland (and really, to the company itself).
4. If the layout is to change, the new layout must maintain the sense of dynamic motion (i.e. some strategic plunging drops) that is lacking in Disneyland, while still being family-friendly. Don't overthink it, don't get too cute, and don't feel the need to compete with TRON or Cosmic Rewind. Space Mountain is a different vibe.
5. If you're going to change the layout, presumably that may also involve getting rid of the bobsled-style vehicles in favor of side-by-side seating. While that wouldn't be my preference (I think the single-file seating adds an extra dimension of precariousness that enhances the experience), I'd accept it if there's the trade-off that designers find a way to keep two separate tracks (thereby doubling the ride's current capacity). I'm not sure if there's enough room inside the dome to pull that off, though.