Personally, I didn't see the need for remastering any of the effects at all. It was certainly a way to make some extra cash off of the old girl and may even have mollified a few of the malcontents who claimed that they couldn't get into TOS because the effects were so "cheesy."
Like everything, TOS was a product of its time. If you're so hung up on making everything look spiffy, let's go back to The Ten Commandments, Cleopatra, War of the Worlds
(original), Day the Earth Stood Still
(original), 2001, etc. etc.
and update all of their effects since they're so badly dated and look so fake. While we're at it, let's replace Bud Abbott and Lou Costello and Stan Laurel and Oliver Hardy (and maybe even George Burns and Gracie Allen) with Jim Carrey and Steve Carell so that the modern audiences can better relate to them.
I guess I agree with your initial premise that it was a waste of time, but I emphatically disagree with your conclusion that the remastering needed to go farther. Just leave the original classic alone and let's appreciate it for what it was.