I love the remastered Blu-rays. When I first bought Season 1, I immediately watched an episode with the original effects shots, and I was absolutely mortified. Obviously those shots were never intended for that level of scrutiny. So ever since, for the most part, I've only watched the remastered versions.
I think the new VFX make the show much more watchable, and the they often serve the story better. With the old shots, your imagination often had to fill in the gaps because they couldn't show you exactly what was happening. Good examples of this are The Ultimate Computer and Doomsday Machine; if you watch the new and old versions side-by-side, IMO the remastered FX give you better and clearer action and do a better job keeping the suspense going.
But if you're a glutton for punishment, just watch the Blu-ray versions with the original VFX shots, or the DVDs as Brian does (which don't advertise the flaws the way the HD versions do).
Regarding the model, the saucer paint is definitely going to be left as-is, except for maybe some sort of treatment to stabilize it and slow down the deterioration. It's the only original paint left on the model, so taking it off would border on vandalism. Everything else is going to be repainted, since the EM restoration took off all the old paint anyway. IIRC, Dr. Weitekamp said in her presentation that EM did that according to instructions from NASM, which was consistent with normal practice at the time.
As for removing other original parts for whatever reason and replacing them with reproductions -- are you serious? That has to be the worst idea I've ever heard.