I always felt that TWOK was a rebbot of the movie franchise and they wanted to ignore TMP. The rest of the original cast movies all flow from TWOK and since the events of TMP are never referenced it could easily be omitted from personal continuity.
I do like TMP though. But its style is so different from the rest of the original cast movies is another reason it could be ignored if one chooses.
I never thought much of TMP originally as it seemed to me too long and rather boring (I mean, Really?!? not one slug fest in the whole picture?!?) However, in last couple of years it's grown on me and It's become one of my favorites.
All that not withstanding, I never considered ret-conning it out of existence because of WOK's superiority. (This is largely due to a couple of my favorite books mentioning the V'Ger Crisis specifically (Time for Yesterday and Strangers from the Sky Both of which occur partially within months prior to Wrath of Khan))