The quality of the writing and performances and cutting and such is the main factor, I agree; but to me, the low-end production values of the live-action TOS shoots are a lot more disagreeable to the eye than most of the VFX shots (about half of which are totally watchable for me) ... on the other hand, the often cartoonish -R vfx have kept me from watching a full new ep in this incarnation, because it is like watching a movie rough cut with animatics in place of finals.
I agree w/ what you've written about the VFX shots. However (and I seem to be in the minority based upon others' posting) I still don't see many glaring issues w/ the live-action shots.
The other day, I saw the first really obvious flaw. In Mirror, Mirror, when Scott and McCoy climb the ladder to the little upper-level engineering room, I could see the seam where two wall pieces were put together.
Otherwise (and I am looking for them), I don't see any issues.