Ever since The Motion Picture
came out on DVD, to my mind only The Final Frontier
needed that kind of re-editing, new FX and reinstated material. Pretty much because to this day the theatrical print looks more like a rough cut shown to test audiences. Paramount should give Shatner a Director's Edition project to work on... keep him sweet, in the light of his non-involvement with Star Trek XI.
I can probably live with kind of HD upscaling I've seen the video age Trek broadcast in. Afterall, we're not talking about the kind of scratches and defects TOS suffered from. TNG/DS9/VOY have been converted to a digital format for quite a while now and most of the FX fit in fine with the movies.