I think it's human nature for creators to want to put their own spin on things. That's why they're creatives in the first place. That's the best thing about them and the worst thing about them. The temptation to do more and to make it "better" is too great.
I feel like the original footage should be upscaled, cleaned up, and let that be the end of it. I think the original model work should be shown as was. Historically speaking, people should be able to see the 1960s version as was shot. Not a recreation of the 1960s footage, no matter how well done.
Once someone starts tweaking, someone further down the line will want to do a better tweaking, and it becomes a slippery slope. Eventually we'll get to the point where someone will want to remaster TOS again, do another TOS-R, and it still won't be quite right.
As a videographer, editor, and (very) independent filmmaker, I prefer to be able to see the evolution of television (and film) production over time. Each of these productions is a representation of the time and circumstances they were made in.
IMO, the approach they took to upgrade TNG was the approach they should've taken to upgrade TOS.