I've never had a problem with Kes being 2 years old, she was clearly sexually mature. The Ocampa apparently have an eidetic memory and an incredible capacity to learn that at least to some extent compensates for their rapid maturing process.
That said, Kes and Neelix's relationship doesn't work for me at all, mainly because there's no chemistry between the actors. The relationship dragged on too long, and I just wanted Neelix's jealous outbursts to stop. He doesn't treat her as an emotionally mature adult and his attitude is paternalistic and patronizing. While some women may enjoy being treated like that, I never have, and seeing it on screen quite frankly creeps me out.
I quite like Kes, and while I realize that there were real-life reasons for firing Jennifer Lien (which audiences didn't know about when the show first aired), I didn't like Seven much when she arrived. The Borg queen started the process of spoiling the creepiest Trek villains ever, and Seven completed the process. The fact that her arrival coincided with Kes's departure didn't exactly help.