Personally, I think that the realtionship was OK to start with but that it was doomed as soon as both of them became crewmembers (or "valuable colleagues") on Voyager.
Kes quickly found a life on Voyager. She started to grow vegetables and flowers in the Hydroponc Bay, then became a nurse. She found friends among the other crewmembers and had no problems at all to adapt to the life on board a Starfleet ship.
Neelix, on the other hand quickly realized that on Voyager, he was basically nothing. OK, he had some knowledge about the part of space they were in, he could find food and other supplies here and there but that was it.
For Janeway, relying on Neelix "only proved fifty percent effective. he got them help some of the time and into trouble all the rest" as it was written in the Voyager book
The Escape by Dean Wesley Smith and Kristine Kathryn Rush.
So in order to show his importance, he became frenzy and came up with all his stunts, becoming cook, naming himself Morale Officer, becoming a journalist and making the program "A Briefing With Neelix" and all that.
Unfortunately, his insecurity also made him extremely jealous when it came to his relation with Kes. That ultimately led to them drifting apart and the break-up was inevitable.
Unfortunately, all of that was very badly handled by the Voyager writers. Instead of breaking up the relationship in season 2, most likely some time after the episode Parturition and doing that during two-three episodes where the reasons for the break-up could have been showed up and analyzed, they let the whole thing hang into the air until season 3 and the episode
Warlord where they did break it up in the most ridiculous way.
Berman, Braga and the other writers were downright lousy when it came to describing relationships, both in TNG and in Voyager. Sometimes I wonder why they even bothered since they couldn't handle it.
Shipping any non-Ocampa character with Kes would have been problematic, because her species has such an accelerated life cycle. Remember, at age two, a human child may or may not be potty-trained. A two-year-old Ocampa is physically (and sexually) mature. A human four-year-old is considered too young for full-day schooling, and may not have outgrown nap time. An Ocampa woman typically becomes a mother at four. And, Ocampa die at about age nine, an age at which most humans haven't even started puberty.
In light of that, I don't see any character on Voyager being anything but problematic for Kes... even Harry was 11 times her age! And Neelix's jealousy only made a dubious situation worse. Maybe Neelix would be more popular if he hadn't made such an... icky first impression. There was, IMO, a lot to like about him.
Ergo, it can be argued that the best romantic pairing for Kes was... none at all.
In fact, the nine-year lifespan was even worse than the Kes-Neelix relationship in its worst moments. It should never have been created in the first place.
Obviously, it was something they came up with just because they had never had something like that before, not realizing that a species with such a short lifetme could never develope to anything more than primates.
And then they did what they always did, just didn't care that it didn't work instead of correcting it by coming up with a way to prolong the lifespan which would have created a lot of opportunities in many ways for Kes.
a two year old.