Phase 2, depite virtually the same sets, music, sound etc as TOS, blends perfectly with the CG. TOS-R does not - but that's probably because of the direction and timing more than anything else.
IMO, the recent Phase 2 episodes ("World Enough..." onwards) have superior CG than TOS-R. The lighting in particular is far superior to some of the weaker TOS-R shots.
Compare the Romulan ship in "Balance of Terror" to the brilliant updated version in "World Enough and Time". I think that sums up the whole argument.
Of course, if you include the early New Voyages CG, TOS-R's consistancy gives it the win.
The fan film with effects most true to original TOS is probably the first Starship Exeter film.