I was going to wait till I caught up to the OP before posting some more of my own thoughts on the closing episodes of S3 and the start of S4, but decided to post things in blocks instead of all at once, so here we go with my own thoughts on Favorite Son through Distant Origin.
I'm pretty sure TOS drew fairly heavily on myth as the inspiration for a lot of its story ideas, but I can't recall it bring done in TNG or DS9, which makes this episode fun because it's basically the Sci-Fi/Star Trek version of the Siren section of The Oddysey, which I thought was cool.
Like the OP, I wasn't sure I was going to like this episode, but I ended up changing my mind. I liked both the A and B stories, although I do have to admit that I was skeptical about B'Elanna being the one to make the alterations to the Doctor's 'Family Life' holo-program.
Tom's continued subtle flirting with B'Elanna was also fun, although it's rather ironic that she'll read Klingon romance novels while shunning pretty much every other aspect of her Klingon heritage.
Before and After
Kes happens to be one of my favorite characters on the show, and I also really like time travel stories, so I was already 'predisposed' towards enjoying this episode even if it had been horrible.... which it was far from.
It reminded me a lot of both Endgame and TNG's All Good Things and Parallels, and the conceit of tying it to the Year of Hell and thereby creating some foreshadowing was a really neat creative decision.
I also liked seeing what Kes would've gone through if she and Neelix had mated during the events of Elogium.
The OP talked about how it was kind of jarring seeing Kes with long hair in the present without any explanation, and I agree, although I also think it works despite catching you a bit off-guard.
I really enjoyed this episode. It reminded me of Tattoo, TNG's The Chase, and DS9's Vortex, and also served as a callback of sorts to Threshold (at least for me).
I also liked the fact that it not only referenced Basics P2 and Fair Trade, it gave us new info about the latter by showing us that one of the items Voyager had used for trade for the items they acquired was a canister of the warp plasma they'd traded for with the Tak-Tak.
The whole 'alien Galileo' ending was also neat, although I really wanted Chakotay to smack the Voth Minister in the face.