My problem is this -
1. From the very beginning, it was setup to look like Janeway might be into Chokotay, and vice-versa.Yes, it could have just been a red herring, but it still made fans think something was going to happen there. This establishes - in our collective consciousness - that they are 'a thing' (even if just wallows in 'what if' land).
2. Janeway 'adopts' seven, very much like a daughter. I think she even tells her this at some point.
3. To us - subconsciously - we now have a scenario where a dude is creepin' on his girlfriend's daughter. Is that what it really was? Well, no... because the J/C thing was just in our heads, but Chokotay was at least Janeway's colleague, 'equal', and friend... and he hooked up with his friend's 'kid'. It just gives Chokotay a creep factor he should have never had. We already had Neelix for that. Kes: "Mr. Neelix, I grew up and I don't really like your lollipops anymore". LOL
Now Harry was also like 'the kid' in the beginning, and Janeway also took him under her wing (they all did), so seeing the 'kids wind up together' would have made sense to our collective consciousness, even though in reality she intimidated Harry, just as B'lanna did. Thus, the series should have ended with ENSIGN Harry - shown grey and half-bald - feeding something in his fishtank... he kept one of the squishy, slimy 'fish babies', and as he feeds them, he whispers, "but you still love me, right?" {fade to black}