In the prime Star Trek timeline, the USS Voyager returned to the Alpha Quadrant because
a future version of Janeway had come back and equipped the vessel with advanced technology such as ablative generators and transphasic torpedoes.
Both proved to be a massive advantage over the Borg, but chronologically-speaking, the film "Star Trek: Nemesis" is the last we see of Federation technology and/or vessels. I haven't played Star Trek Online or read any of the post-Voyager novels, but I would expect Starfleet to utilize such an advantage - especially with such powerful enemies as The Borg and The Dominion around. Concerns about the temporal Prime Directive wouldn't seem to apply, given that the timeline in question had already been changed and/or erased.
In the Prime timeline, are there any mentions of Starfleet deploying the technologies used by Voyager after its return?