I never had that feeling. I was absolutely sure that both of them would be on the ship when they arived to Earth (and honestly, they should
have been there too).
Neelix stated many times that he would stick with Janeway and the others. Kes was as eager to get to Earth with them too, besides that she wanted to learn and explore. And after "Cold Fire" I was absolutely sure that they would find a way to prolong her lifespan.
The short lifespan was a big mistake, the worst flaw in the character. To be honest, a species with such a short lifespan could never develope into more than primates. Not to mention the error with the "one-child" syndrome. Sometimes I wonder if the writers really did know what they were doing.
Anyway, those errors could have been corrected.