So touching on a few points of interest:
RE: Janeway and Chakotay
I hadn't actually ever heard about Mulgrew putting her foot down. That makes sense in retrospect that something behind the scenes happened because that pairing frankly seemed perfect ever since Resolutions
in Season 2.
Any other pairing with Janeway felt unnatural after Resolutions
RE: Chakotay and Seven
I absolutely agree that this seemingly came out of no where. Yea, there was some plot development, but not enough. Frankly, realistically, the way things went down, I would have more expected Seven to become infatuated with Chakotay and for him to pull the "You're not my type" card. Let's face it, up until that point, Seven and Chakotay weren't exactly in the same clique on the ship.
The being said, I expected Seven to end up with Harry. Right on from The Gift
the two had one of those awkward "I'm attracted to you, but I can't figure out how to express it in a way that doesn't make me out to be a complete fool" things going on. Like Toress and Paris, I expected them to eventually figure things out and get together.