The question is ludicrously stupid. Choice A hot cyborg babe, choice B frumpy and grumpy general Janeway. The real question should be why did 7 choose Chakotay instead of one of the male crewmen who actually produced testosterone.
These ass-backwards priorities would work on a character that's a 13-year-old kid in our time, but since these are mature adults who live in the enlightened 24th century where hopefully Looks (and perceived amounts of testosterone) Aren't Everything, I'm going to go ahead and say the question
isn't what's ludicrously stupid here.
I honestly think it was meant as an inside joke and big "F-U" to Mulgrew for not allowing Janeway to have an on going romantic interest like they wanted. I think they wanted to get Janeway & Chakotay together for a long, long time and Mulgrew heatedly refused every time. The writers knew J/C was part of the dynamtic that could have improved the show and brought in more viewers. So their answer was to Mulgrew was, then Janeway will never have him and paired him up with Seven instead. So because Mulgrew wanted Janeway to be all career, a career is now all she has.
Plus it being the last ep., Mulgrew couldn't debate it.
This is all just made-up. KM's said over and over again she A) helped with "Endgame" and B) Likes "Endgame," even if the fans don't, and C) Likes the idea of C/7. It's Ryan and Beltran who usually comment on how C/7 was too out-of-left-field for them.
EDIT: The writers were clearly pushing for J/C and she pushed back, but I doubt they'd want to get rid of perfectly good UST by making J/C openly get together any time before the end anyway.