That was partially because Beltran was a b*tch on set and squandered any chances he was given to do anything so they stopped caring.
Also, it was because they didn't do a good enough job making him that dissimilar from Janeway in the first place and were afraid of the underlying sexism of the premise (A weak woman captain who has to compromise with terrorists).
I think that it was the other way around. Beltran maybe did become "a b*tch on set" in the last 2-3 seasons because they didn't care about the character, shoving Chakotay more and more in the background. I can understand that he was upset about that.
Chakotay confronts his lover on her betrayal and using of him. Should have been a great scene except Beltran delivers it with all the emotion of a cigar store indian. It's AWFUL. And it's season one. So this stuff about how poor poor Beltran got pissy because he was sidelined is only half the story. He was sidelined I suspect because he was terrible! Just like Picardo got more and more limelight because he was fantastic. Writers aren't going to write dramatic storylines for people who can't deliver.
I don't see any problem here. Maybe he was supposed to act this way, being in shock over the fact that his former lover tuirned out to be a traitor.
I can agree that this scene is not convincing. But check out Caretaker! Check out Beltran in "Maneuvers" and when he hits Dalby in "Learning Curve" or the episode "Nemesis".
I think that he delivered in most of the early episodes.
As for NuBSG, I'm actually happy that Voyager never got close to that kind of doom-and-gloom show.