The Kes/Neelix relationship was logical in the beginning. Kes saw Neelix as a very exciting person who had seen everything and been everywhere, something she wanted to do herself. Neelix found her very beautiful and was in love with her for that reason.
But when they came on bard Voyager, their lives went in different directions. Kes adapted quickly to her life on the ship while Neelix obviously had some difficulties to fit in, therefore his almost hysterical whims about being cook, Morale Officer, journalist, Ambassador and constantly harassing Janeway, Torres and especially Tuvok about work in Engineering, being on the away teams and so on.
On top of that we had Neelix jealousy and his attempts to supervise and control her which put a strain on their relationship early on. As I see it, it took almost too long before it broke up. It would have been logical with a break-up after "Parturition".
One sad thing is how the break-up was handled. Kes breaks up with Neelix while she's controlled by Tieran and no explanation why their relationship remained broken up after Kes being restored to normal. There should have been a proper break-up in season 2, which should have been more carefully explained and developed in 2-3 episodes. But the writers obviously had difficulties to handle romances and break-ups, something we did see in both Voyager and TNG.