I have no problem with the superimposed images of burning buildings while Bele and Lokai blindly stumble through the Enterprise's corridors. As far as I'm concerned, that's one of the best (and very patently '60's) images of that ep. I say: change it only if you can superimpose even better imagery of the same thing, otherwise, leave it be.
I think they can have some fun with the Enterprise at Warp 10, if they show some imagination.
It would really be neat if the orbital shots of Cheron could show massive devastation of coastal cities from space. That could be a powerful new image to show.
It would be neat if they could also touch-up the self-destruct sequence. The strangely musical nature of the computer during that Cold War-ish ritual was always fascinating to watch. If they can improve the destruct graphics on the panels a bit, that would be a nice touch.
The decontamination of Ariannus will also be a challenge to re-FX. Believe it or not, I'm very fond of the old FX.