The biggest TOS-R gaffe for me was in "The Paradise Syndrome," in which Miramanee specifically says Kirok should go to the temple and make the blue flame come out. For no good reason and in ignorance of the dialogue, they changed the beam to orange. That's a goof.
I understand the loss of live-action-to-fx film dissolves was unavoidable, and yes it's a loss.
On the other hand, there are cases in TOS-R where old mistakes are corrected. For instance, in "Let That Be Your Last Battlefield," Chekov looks at the main viewscreen and says "I think that may be a Star Fleet shuttlecraft." In the original version, the fx shot was a close-up, so obviously a shuttlecraft that Chekov's line makes no sense. In the TOS-R version, the craft is shown from a distance.
I've seen several cases in the original where they simply didn't have an fx shot that was just right for the dialogue, and the TOS-R version took care of it. I just can't recall them specifically. But they're there.