New Trek doesn't do it for me. May look stunning, but it pisses all over Trek history and presses the massive big red reset button. Old Trek is dead now (thanks to Enterprise) and new Trek is just too 90210 for my liking.
But anyway, as for the old, problem is as I understand it, Star Trek: TMP is presented in the rather dull theatrical version and not the much superior Directors Cut (which contains a rare example of how to do CGI enhancements correctly so they don't look out of place and actually improve the film - take note Mr. Lucas

). Likewise Star Trek II is also not the Directors Cut although in this case the extra scenes in the DC are not all that great, but I've been used to them from old showings on TV of the extended version.
I'm not sure but Star Trek VI might also just be the theatrical version which is a shame as the DC has a couple of extended scenes which are worth it.
So, I'll be waiting for the extra special editions with all this restored, much like how I waited years and years for the SEs on DVD knowing full well they'd do them.
Now I know that Star Trek: TMP's CGI effects were apparently mastered in standard def so that's a problem, but with enough demand (or potential to make money) they can redo them. Sadly Robert Wise is no longer with us though and it was his involvement in the DC that really got it off the ground and so lovingly made. Given Blu-Ray sale potential is tiny compared to DVD also, there is less incentive.