In the pilot it was worse, because there he came off as cunning and competent perfectly willing to use people to get what he wanted and stuff. He ever show that level of competence after that?
He had a lot of useful skills that he demonstrated or developed over the course of the series, including engineering knowhow and diplomacy (remember, Janeway appointed him
Voyager's official ambassador). He was a good father figure to Naomi. He applied himself diligently to tactical training and could handle himself in a fight. And he did a pretty good job as morale officer a lot of the time. And he did seem to be a skilled cook; it's just that the types of cuisine he was trained to prepare were aimed at a rather different palate than the Starfleet crew had (which kinda reflects poorly on Starfleet; you'd think they'd be more accustomed to exotic cuisine). In most respects, he was good at what he did, he just did it in a way that differed from Starfleet norms. The one thing he was ever really portrayed as less than competent with was relationships. Well, that and self-esteem, but those were related problems.
Uh.. Neelix was a first-class jerk really. Think about it. First episode we see to him, Janeway asks him to lead them to the Ocampa. Instead he lies to Janeway, leads them to the Kazon, starts a fight with them, all to rescue his girlfriend. He then justifies it that since it turned out alright, it doesn't matter. Frankly, I have no idea why Janeway trusted him after that. Good diplomatic skills there...
As for morale officer? He even annoyed Harry Kim in that role, and that takes some effort since he's pretty much the most tolerant guy on the ship. Really he tries to force his values on people. Tuvok's a grand example of this. He constantly is trying to "cheer" him up when doing so is culturally offensive to Vulcans. That Tuvok's values are different from Neelix's is irrelvant, Neelix just has to force his values on everyone.
Really that's his style in everything. He forces himself into any given situation, and then tries to lord it over everyone. Be it the meetings, the bridge or the kitchen. He comes in uninvited, and will either force his opinion on the people, or just critcize what the crew is doing. His behavior in the kitchen is a good example. Telling people they can't use replicator rations? Isn't that the whole purpose of a ration? To use when you want? Up to the person, not the bleeding cook, to decide if they want to save them or use them at once. Everytime someone walks into the kitchen that's not part of the crew he instantly gets territorial as if he was important. Further evidence of this is whenever he tries telling people what they should and shouldn't eat and when they should or shouldn't eat. He's the cook, his job is to make food for people. It's a big ship with rotating sleep schedules. People are going to be eating at all hours.
His possessiveness with Kes is just retarded. This guy should just be thankful he has a woman who seems interested in him. Instead he is controlling to the point of almost abusiveness. It really says a lot about Neelix that he goes after a short-lived naieve race. Heck when they first met, Neelix must have been the most interesting man in her small world. The guy from space... until she just later figured out he was a glorified garbage man. Even for a race that doesn't believe in seperation, after Kes was controlled by that evil emperor alien and broke up with Neelix, she just went along with it. I can't blame her.
As for applying himself diligently to tactical training? This is just another example of him forcing himself into any given situation. And lest we forget... the guy is a draft dodger. Not only did he refuse to serve in his homeworld's military because he thought the war was "wrong" it led to the conquest and subjugation of the said homeworld. Yeah, good material for a security officer. Declaring the war immoral when they conquered your world? I'd call cowardice a better reason.
He's really the nosy neighbor type that just has to poke his nose into everything, without any respect whatsoever for people, their opinions or feelings. He was right and everyone should listen to him for their own good in his deluded world.