Actually make Kes a child
The issue with Kes' age wasn't her age, but how she was portrayed as an "adult" who could engage in romantic relationships. It made people feel weird. So a way to change that is to just make her an actual child. This goes without saying, but we'll say it anyway, that it changes the romantic relationship between Kes and Neelix into a more paternal one. Maybe you drop the Ocampan idea and make them both Talaxian, or you make them both Ocampan and actually make them a father and daughter.
Another idea is to just do the Naomi Wildman story earlier. Naomi Wildman was such a breath of fresh air in the later seasons, but what about starting from the jump and bringing on a child actor to play Kes? Have Neelix find Kes in the pilot and have him essentially be a godfather/surrogate father character to the younger Kes. Get rid of any romantic ideas and just make it a paternal bond, one where Neelix is compelled to protect the child Kes, and not try and date her.
Granted, it may be too close to how they used Wesley Crusher in The Next Generation or Jake Sisko in Deep Space Nine, but what you lose in originality, you make up for in lowering the "cringe levels". Plus, maybe Neelix is a bit harder, having protected Kes for an unknown length of time, and is far less of a suck up.
And that leads us to our next idea, which is similar to this one but doesn't change Kes' age.