The idea that Spock would stop aging because he was moved away from the genesis effect has from day 1 sounded as preposterous as anything else about Genesis. What, does that mean if Spock gets near green protomatter he'll suddenly start aging again? It just sounds like contrivance on top of contrivance, and arbitrary as hell.
Your other criticisms are valid for the most part (Valid enough that I don't feel the need to argue against them). Yet all of them I either never noticed until they were pointed out, or never bothered me that much. Except the one I quoted above. The logic in this bugged me when I first saw the movie when I was 11. It never made much sense to me & I never felt the concept (if there was one) was explained very well. I love TSFS, but this is the one major blemish I see in the film.
"Canon is only important to certain people because they have to cling to their knowledge of the minutiae. Open your mind! Be a Star Trek fan and open your mind and say, 'Where does Star Trek want to take me now'." - Leonard Nimoy