I can't comment intelligently on Ethan Phillips except to say he's an actor and paid to do what's on the script. If he said he was trying to make the character come off as annoying, well I'd say he did a fine job of it.
I can intelligently say the writers made the character screwed up to the point where I had little sympathy at all for him. Frankly, it still baffles me why Janeway ever trusted him and took him along after that crap he pulled in Caretaker. He deliberately misleads the crew about where their people are and brings them to a Kazon camp to rescue his girlfriend. This gets them captured, he escalates the situation by starting by taking their leader hostage, and quite nearly gets the whole away team killed. Then he acts as if it was no big deal and that their problems don't concern him now that Kes is safe. Even Kes had to point out how much of a jerk he was there. He could have just been honest and said these bad aliens have his girlfriend captured, and she can lead us to the people who have your friends. But that would've been like... honest and respectable.
To the episodes listed as good "Neelix" episodes let's see....
Jetrel, this was a good episode. Though how Neelix can be so righteously upset about it when he was "against the war" and draft dodging is far fetched. Jetrel carried the episode with his desperation, and Neelix... I dunno, just came across as petty... even when he thought they guy was trying to save his life he acted quite... childish towards the man. It was a good overall story though and easily one of the best of season 1.
Tuvix- To be fair wasn't really a Neelix episode. Tuvix did demonstrate some of Neelix's characteristics, but... in moderation really. Which made him less annoying. Then Janeway had to murder him. But there's morality for you.
Fair Trade- I do dislike the Neelix character a lot, but I did have to feel for him in this episode. It's easy to see how he got caught up in this, just one bad call spiraling more and more out of control as he gets deeper and deeper into it. You could kind of sympathize with Neelix's thinking that he was worthless and was trying to stay useful... especially since his own expertise is generally just him talking up his abilities to make himself look good.
Mortal Coil- Really was just a bleh episode to me. Between an overexposure of Neelix, to great forest stories with Naomi and another technobabble cliche save his life plot, it just didn't engage me. A few interesting character details just aren't enough to carry the episode or really make me receptive to the antagonist of it.
Once Upon a Time- Yeah this story combines annoying children and Neelix set in annoying holographic childish setting. Yeah... I didn't care for this one. Any drama with Samantha's imminent death was not enough to detract from the annoyance of watching this one. Flotter... even the name is annoying.
Riddles- This one sort of grew on me over time. The alter Tuvok is kinda fun, and Neelix, while at first engages in his sick fantasy of having Tuvok remolded into an image of himself... he does eventually do the right thing and persuades the alter Tuvok to do the procedure. So his jerkishness has limits at least.
Homestead- They're supposed to be 20,000 light years from Talaxia by now so this one kind of stretches credibility, but we can role with it. Neelix was his usual overbearing self to Tuvok... and Tuvok really shows what a great guy he is... by giving Neelix the confidence he needed to help the Talaxian and even unwinding enough to dance when he was leaving. As much as I want to say "YAY he's gone!" you can understand his decision... this literally is the last chance he's gonna have to be with his own people. So I'll say I liked this one overall. Nice of them to remember they've been hauling Neelix's little shuttle thing all this time too.