I also hated a few of the episodes they did. Should they change them for the remastered?
Sure, why not?!
...Is your question supposed to imply that any new effects work should mirror the old ones so pefectly that they use two distinctly different CG models? Or is this just a "No new effects work at all!" thing?
My point has been all along that they should re-use the original footage, as they shot the models on film, just composited them on video. So they need to scan the film and re-composit the effects in HD. That way they use as little CG as possible, and keep the show with the original effects intact. Planets, suns, nebulas, shield effects, phasers, torpedoes, explosions, etc... would have to be done with CGI of course (unless they have been filmed, too). But the model work is perfectly fine on HD.
would turn into this: