Another problem was the egotistical Shatner. As the series progressed, he and Nimoy became such pivotal characters. And Shatner exercised his power often, having things changed here and there to suit his desires (and ego). The idea of a non-primary character getting extra attention pissed him off.
Let's not drink too deeply from the "Shatner done us wrong" Kool-Aid. The stuff that Shatner had cut was stuff that bogged down the story and really didn't serve any purpose, i.e., characters being given lines for the sake of being given lines, whether it makes any sense for them to pipe in at that moment or not. And by that criteria, we're talking about dialogue that probably would've been chopped during editing anyway, so why waste the time, film, and more importantly, money in filming stuff you know is gonna get cut?
I think Shatner's theory is correct. It wasn't until the conventions, with thousands of screaming fans telling the various cast members "Scotty/Sulu/Uhura/Chekov was my favorite!" that the resentment started kicking in. Before that, you never heard a peep and it was all one big happy family on the set (a version that's pretty well backed up by folks like Eddie Paskey and Billy Blackburn, who haven't been puffed up by forty years of con puffery and probably have a clearer recollection of events, not to mention Blackburn's home movies from the set).