Though it would have been rather dissatisfying in a series finale, it might have shown strength of character if Captain Janeway had refused to alter the "proper flow of events" by getting Voyager home earlier. In any event, the ending as shown is dissatisfying to many viewers who wanted more of a resolution than simply "they get home." To the question of whether Admiral Janeway ultimately altered her timeline or an alternate - does it matter? The point would seem to be that Captain Janeway knew that following Admiral Janeway's advice meant acting against what was "supposed" to happen. Unless you want to try to argue that this was a predestination paradox.
You know, sometimes I'm left with the feeling that going up against outspoken fans of Janeway is as much of a pointless endeavor as going up against the harsher critics of the new movie. Nobody's opinion seems likely to change, and there ofter never seems to be any willingness to concede that Janeway even -might- have made a mistake. Nowhere have I said that Janeway -definitely- made things worse, I just refuse to whitewash her actions and ignore the glaring possibility that she -might- have.
In "Insurrection", Picard asks the Admiral who wants to relocate the Baku how many people need to be relocated before an action becomes wrong, regardless of the positive consequences of this relocation (and the relocation apparently could have positively affected a huge number of lives).
How many lives do Admiral Janeway's actions need to negatively affect before they become wrong? Is letting two planets dissolve into war because Voyager wasn't there to mediate enough reason? Preventing a planet's population from dying because the ship wasn't there to help develop a cure? We have -no- idea how much good Voyager may hae done, and just as it's impossible for me to say with certainty that Voyager's aborted journey had negative repercussions, it's reckless for the supporters of Janeway's actions to claim that there could be only positive repercussions. -We do not know-.
What -do- we know?
Janeway doesn't appear to have been motivated by a desire to improve things on a grand scale. The Federation appears to be doing just fine, and there's no mention of any significant problems being faced.
Janeway clearly acted without any sort of authority beyond her own self-righteousness and without any regard for those whom her actions might negatively impact.
Anyway, at least Annorax -did- gather souvenirs before wiping planets from the timeline. We have no reason to believe Janeway made similar efforts to memorialize potential victims of her decision. Perhaps we'd be better off if it had been explicitly stated that Janeway's time travel methodology would create an alternate timeline rather than overwriting what we'd seen.
Look, I'm really not trying to be an outspoken critic here, but I feel like I'm going up against a bit of a brick wall of refusal to acknowledge that what Janeway did could be anything but positive, yet with little information to support that hypothesis.