Make Neelix Kes' protector, not lover
Neelix worked best as Naomi's godfather and overall protector of those who were a bit socially awkward. Not to mention, no one thinks raging jealously is a good trait. So instead of having Neelix less mature than a two-year-old, have Neelix actually serve as Kes' protector and surrogate father. With so much turmoil in the Delta Quadrant, it's not out of the realm of possibility that the sector tormented by the Kazon would see a lot of death and subsequent orphans.
Having Neelix find Kes, and take her in, serving as a father figure, would have been a heart-warming scene and would've established Neelix as someone who wants everyone to be safe and happy. Not some weird creep who fell in love with a two-year-old. You'd be able to do so much more with the Neelix and Kes pairing this way, and it would even work if the goal was to bring in Jennifer Lien to play the character.
If the original formula for Kes and her species was to have a short shelf life, Neelix as her protector would still work. Now, some, including Ethan Phillips, would argue that it was part of the dynamic, we know that's not true. Kes went into heat and asked Neelix to mate with her so she wouldn't miss the chance to be a mother. You're not asking a parental figure for that type of assistance.
Clearly, they had a romantic relationship and that relationship made everyone uneasy while they were watching it. Yes, space customs are different but most of us aren't down for even the concept. Having Neelix protect and watch out for her would've made him far more likable from the start. It was the perfect role for his character in the later seasons and would've worked perfectly for him from the jump.