Another example of the timing being off for the new effects was in Mudd's Women. After they beam Mudd aboard, but just before they snag the chicks, Mudd's ship is hit by an asteroid. In the original, Farrell cries out "there she goes" By the time Kirk turns around, he see what we see: the ship exploding. Not the impact itself, but the result.
In the TOS-R version, Farrell cries out "there she goes," Kirk turns from Spock's scanner, looks at the screen and the asteroid STILL hasn't hit the ship yet, it strikes a second or two later so the audience can see a "cool" visual. However, when Farrell cried out, the asteroid was still a ways off from hitting the ship, so yelling out "there she goes" makes little sense. Yes, I guess he could be anticipating and making sure Kirk doesn't miss it, but that is another excuse for bad effects judgment.
I guess it's just me, but the new ship explosions never looked quite right. Far too quickly done and very Babylon 5 like (their ship detonations were pretty phony looking even for the time). I found the Klingon ship explosion in Day of the Dove to be very unsatisfying; we see the ship for a split second, not long enough to process the image. Too short to even justify drawing it.
However, some of the new effects are stunning. The Rigel 7 fortress, the Enterprise in Tomorrow is Yesterday and so on. But being complimentary is boring. LOL