I was watching TOS HD a bit recently and frankly I prefer the old effects shots. I just don't go nuts for CGI anymore. TNG had some pretty decent model work, amazing for TV. The time and money constraints were crazy. The results are worthy of admiration simply because of that.
If they do redo it all in CGI, I hope it's much better than TOS HD and better than the shot of the D on the last Ent episode. No fakey lighting. No plastic look.
And yeah the 3D fad isn't really for me. I didn't even think Avatar's 3D was all that mind blowing honestly. It's hard on the eyes. And if the production isn't filmed with it in mind it's just gonna be a hack.