Well they still need to keep things fairly consistent, I think. If they're going to dramatically sharpen and clean up the planets, transporter beams, and other energy effects (which I am eternally grateful for), it only makes sense to improve some of the shakier model effects as well.
Otherwise they're likely to stand out even MORE.
They're doing that stuff solely because it doesn't exist in a form that will translate to HD. The model work will.
Is this desire to "fix" stuff a Trekkie thing? Are there blu-ray forums filled with people wanting Alien or Total Recall or Tron fixed up? Special Editions don't really seem to fly. The Star Wars fans seem to get that now. ET 2002 won't even be on the new BR disc. When I personally watch a BR movie or see it again in the theater I'm doing it because I want to see what I've been seeing in SD in a sharper form. I don't want to see something new. If I wanted to see something new I'd watch a new movie. Does that make any sense?
2012 effects added to TNG will look as bad as the original stuff in ten years time (if not in ten minutes). If the remasters are eventually going to look bad, shouldn't it be with the original work in it?