With the early Voyager episodes, I thought the Neelix and Kes romance worked, though it should be noted I don't care for love stories.
I'd always thought of them as a couple, so it was somewhat of a surprise when there were suddenly Paris-Kes subplots with Neelix now out of the picture. Were there any hints of an impending break-up? I understand the actual split was done off-screen, but it really was awkward. It made me dislike Paris for it, which I don't think was the writing staff's intent.
Edit: I vaguely remember one episode where Neelix and Paris get in a big physical fight over something.