I know we were kinda 'stuck' with using Q as part of this, seeing as how Janeway finished her previous appearance, but it ends up being hard to avoid the 'deus ex machina' feeling that way.
Honestly, had no problem with the Janeway parts, that was handled about as well as you could, all things considered. Introduced pretty well, people had the right reactions, etc.
Thought Cpt. Eden's storyline ended abruptly, and wish we'd had more time on the scavenger hunt for her origin, over more books. Along with the Borg, that was the fun of her character. Guess she had to go to justify Janeway hanging around, but miss the interaction there, and the hunt.
Again, problem with using Q is that things end up arbitrary. Hated the Amanda Rogers death. Deleted from existance, never even existed. It's fine in the sense that they were deleting the spawn of both Q and Omega at the same time, but her death really wasn't given any weight. it's like she went off to go investigate something, and then just never turned up before the end of the movie. Expected more interaction from her in the Omega sections, or at least some impact over her death. She just turned into a throw-away.
I'm sure we'll find out that most of the favorites were saved when the 4 ships were blown up, but still felt like too much. Had most of the ships escaped and only ONE got stuck/blown up, it would have had the same impact. Just feels like we killed the whole point of the DQ mission, and disbanded the fleet. Sure they'll send a replacement ship along with Achilles back, but then what's the point of blowing them all up to begin with? Just felt like a waste, and rang hollow anyway. Spent all that time in the last book rebuilding the crashed ship, and it only got like 4 more pages of screen time before being blown up again. Were made to care, and then there's not enough payoff to justify it.
Chakotay's "death" - seemed pointless. No emotional impact, and immediately undone anyway. Wanted to care, given the empty hint to Janeway that her rebirth would have a cost, but we all knew he wouldn't die, so why send him? Biggest benefit of bringing Janeway back is to explore the relationship, so you weren't going to kill him. Would have been a bigger scene if you picked the new helmsman, that way you at least get a 'named' character to dangle. In-universe, justification was that she was needed to get Voyager to safety, but Paris could have handled that. Then at least we would have been worried that she may actually die, despite Jr. bringing her back.