You're forgetting the horrifying skin rash. Regeneration doesn't fix or clean teeth. True, she hadn't eaten anything for twenty years, but she had been walking around in a vacuum now and then which must have ripped the enamel off, burnt them with radiation, and frozen them brittle. The Doctor made her hair, and probably gave her new teeth as well.
I think that the true problem here is that Voyager through its producers/writers, too much calls on the principe of timeline changing in its storylines at the risk of reaching saturation. Indeed, the timeline changed so many time that even the end proposed in Endgame puzzled me because soooo irrealistic so much the consequences for each protagonists are minimal with a happy end for everyone.
In Renaissance Man they mentioned the border of the Beta Quadrant. Once they crossed that line in space, it was nothing but Romulans and Klingons, the federation's allies from the Dominion War. Plain sailing. Also they were 4 years from Rendezvousing with Federation support Vessels as mentioned in Life Line, unless one of their Short cuts, made that meet and greet difficult.
As my experience with Star Trek is quite limited (I just stuck with Voyager because of Kate Mulgrew's acting), I don't know what's going on with the other series of the saga but already with Voyager, I was fed up with all the timeline changing at the end. That being said, I remember to have watched a movie (sorry I don't remember the name but the storyline trully marked me a lot) where a group of young people did their best to avoid the brutal death which was planned for each of them and at the end, despite all their efforts to change the timelin and the event, they died in violent circonstances, worst than what was originally planned. The dark moral of the story was something like "no matter what you do, your fate is sort of already written in your genes. Don't try to change history to save you skin, it won't work and just risk to turned against you".
Optimistic In a fusion of Timeless and Galaxy Quest, the USS Voyager gets into a fight with a Borg cube while moving through the conduit. Eventually the cube is destroyed, but a few drones manage to latch themselves onto Voyager's hull. Emerging from the conduit very close to Earth, the ship manages a crash landing in San Francisco (you could even have it at the Golden Gate Bridge). Janeway and company step out onto the steaming primary hull to shoot down the surviving drones. They then find themselves surrounded by a cheering crowd, including all the familiar faces from TNG and DS9. Pessimistic The Borg damage Voyager enough that she loses navigational control and a warp core breach is imminent. The ship emerges from the conduit too close to Earth to stop in time, slamming into the ground at transwarp velocity. The warp core explodes on impact along with any unspent transphasic torpedoes. The camera pans out from Earth, which exhibits an enormous smoking crater where California used to be.
I generally I like a happy endings, so I would have liked the ship to get back in one piece with the whole crew intact. But I like the idea of not using the "Janeway of the future" approach. I would have made it a three or four parter, gotten rid of the Janeway of the future as you suggest, use your suggestion that they find the damaged hub, but pretty much keep most of the rest of the plot intact, just using the present day Janeway. I think what turns most people off of the finale is that they're "rescued" instead of getting home on their own.
I tend to be one of those who just likes each series, and doesn't complain too much about episodes or arcs... my intense dislike of DS9's doctor (and actor) notwithstanding. But someone brought up the idea of not using the time travel approach, and instead have Voyager detect a malfunctioning trans-warp hub they repair and attempt to use. Most of the rest of the plot would be the same except for the Future Janeway. The only problem here is technology to keep Voyager from being assimilated as they confront the Borg. Not a bad change, I think. And it would remove the feeling that Voyager was just "rescued".