I think in a way you're both right. I think part of it is sometimes fans, including myself, don't always understand all the ins and outs of what goes to make a show.
That's true enough. Audiences only see the finished product, so they see it as a singular thing and have a problem with changes. Creators, though, understand that the finished product is the result of a process of experimentation and revision, the final draft of a series of drafts or the final edit of a series of edits. So we're open to further revisions to improve it as we go, even if they're retroactive.
You could probably find an equal number of people that would love it if they threw everything out, made Klingons amorphous blob people and give Vulcans 3 heads.
If I could reboot ST from scratch, I'd make aliens like the Klingons, Andorians, and Cardassians nonhumanoid. I'd also set it much further in the future so that humanoids like Vulcans would be human colonists genetically engineered to fit new environments and developed into distinct, independent cultures over a millennium or two. Which would make it easier to justify interspecies hybrids like Spock or Troi, although K'ehleyr or B'Elanna would be out of the question.