I liked how real the Neelix/Kes relationship seemed. Don't take that as I thought they should've stayed together, just that the relationship and it's evolution was pretty realistic.
Look at it from Kes's point of view. Despite the fact that Neelix was basically a glorified garbage man, he was literally the most exciting man Kes had ever met. He lived among the very stars she had dreamed of all her life. His embellished stories of adventure were no doubt very appealing to her and their life on Voyager was to be yet another adventure.
Neelix really did it to himself in the end though. He was possessive to the point of stalking her. He got jealous if she even talked with a member of the opposite gender, and generally was overbearing. Sure, it did take an alien possessing Kes to dump him, but she stuck with it afterward. That's quite telling considering she said Ocampa mate for life.
To me it was as if Kes had outgrown Neelix. No longer was she the innocent girl, coming along with Neelix on an adventure. She had matured, was exposed to plenty of adventures in her own rights, had her own sense of self worth, and though it took an alien possession to do the deed of dumping him, the thought was already there being she didn't go back to him. Her world had gotten so much bigger from when she had first met Neelix, and that made him only so much smaller.