Kes definitely annoys me with Mary Sue vibes, at least in some episodes (like "Before and After," despite the fact that I love that episode). And the worst thing is that on paper, Kes's background should make for a VERY flawed, interesting character. But none of that was ever explored. Instead everyone on the ship just instantly liked her (despite her species indirectly being the reason for Voyager being stranded); she had no problem socializing with the crew (despite her background and biology); and all of her personality traits are gushing compliments ("determined/beautiful/kind/brave/strong/powerful
/mysterious...blech.")
BUT, as someone on this site pointed out, Kes overall lacks the spotlight hogging that a true Mary Sue would have, so I'm now on the fence about her Mary Sue status. It's weird, but for how much people gushed over her when she was in the room, no one ever seemed to specifically seek her out to help with a situation where untold mental powers might be useful. It's almost like the other characters (or the writers?) were just trying to make Kes feel good when she was in the room. (Maybe they pitied her for her short lifespan?)
In short, I don't think the writers built Kes up because they were in love with her, I think it was the opposite. She was a convenient tool for the other (male) characters. This perfect, idealistic girl for Neelix to be jealous of, and for Tom and the Doc to long for; "mysteirous" powers vague enough for the writers to write themselves out of any corner; and gushing over how great she was almost seems patronizing, like a lazy attempt from the writers that this really is all for the sake of Kes's character, and not just the plot.
("Hey guys, Kes, just discovered another power! We'll just, um, tape that power to the 'fridge, so everyone can see how pretty it is. We really respect you as a character Kes, honest.")
So in the end, I guess that could make Kes...what... an accidental Mary Sue? It's a funny irony, that they made this character annoyingly perfect because they simply never gave a damn about her. Had they cared to actually do something with the frankly interesting backstory she had, she'd be one of the most flawed and lovable characters in "Star Trek" (similar to Trance Gemini from "Andromeda"), and she and Seven could have played off of each other wonderfully.
Jennifer Lein deserved better.