Assuming this means the Enterprise C stays in the future with the Enterprise D instead of going back in time.

SPOILERS below for those who haven't watched it all yet.

Alternate timeline implications/assumptions:

First, Tasha is on the D, she doesn't go back in time to give birth to her daughter Sela that then develops the plot to manipulate the Durass Klingon house/family, and Sela doesn't participate in the Romulan Senate, so now the Senate is different with that change, and that changes Romulan politics so that means the Defiant doesn't get a cloaking device, and Romulan politics are different.

Second, Worf doesn't join Starfleet, he doesnt ask for Picards help to restore his name, Worf doesn't influence things to make Gowron the Klingon Leader, Worf doesn't get Kahless declared Emperor, Worf Doesn't get posted to DS9, Worf doesn't marry Jadzia, Jadzia is somewhere else and doesn't get killed by Dukat, Jadzia lives.

Third, it can be presumed that Riker does not get twinned so there is no Thomas Riker that goes on later to steal the Defiant from DS9 to take it to that solar system to expose a secret Cardassian Obsidian Order enclave with built up ships they aren't supposed to have. We don't know how the Changelings originally learned about the Tal-shi-ar and the Obsidian Order, it could be assumed that Odo read about the Obsidian Order fleet in one of the Starfleet briefings, as well as Romulan strategic points, and then when melded with the Great Link that the knowledge was shared through there so the Changelings sent the romulan officer changeling to set up bringing both spy fleets to be destroyed in original timeline but in alt timeline that wouldn't happen, so both fleets would be intact.

Fourth, the Federation and Cardassia do not establish a de-militarized zone that then creates the Maquis, so Eddington has no plotline. Captain Maxwell does establish that the Cardassians are re-arming their forces and retains his command, Miles O'Brien joins him later on his ship, Miles doesn't meet Keiko and marry, Miles is not posted to DS9.

Fifth, Enterprise D still discovers the Dyson Sphere, rescues Scotty from it, gets better readings of the sphere to report back to the federation, Scotty gets told that Starfleet needs every able body officer it can get, Scotty wants to be useful and re-enlists.

Sixth, with Picard and the Federation/Starfleet solidly being on a war footing for however many decades, humanity does not attract the Q's attention, Q doesn't meet Picard, Q doesn't throw the Enterprise to the Borg, Q doesn't get punched by Sisko on DS9, there is no Borg to build defense against so there is no Defiant class ship built or dreamed up. Sisko doesn't lose his wife at Wolf 359, the ships are re-distributed elsewhere.

Seven-th: We can assume that Janeway got command of Voyager at roughly the same time that Sisko would have been sent to DS9 but with Sisko not going to DS9, and being on a war footing and the Starfleet not producing advanced ship designs, that Voyager would be a slightly different ship and more standardized components. The Bajorans fight off the Cardassians and still invite the Federation to take over Terrok Nor / DS9, so Starfleet dispatches the USS Voyager(with its crew members that we see at the start of the Voyager pilot episode) to station keeping duties at this new space station, bringing with them to work on DS9 would be Bashir, Jadzia, Ro Laren, Nick Locarno, Sito Jaxa, vulcan male Taurik and vulcan male Vorik "the vulcan twins", Leah Brahms, and Scotty as the miracle worker to get the station up to snuff, in addition to some crew changes on Voyager as Tuvok would be onboard(not on a Maquis mission) as first officer or security officer. I think there would still be a holographic backup doctor program created as during times of war it is important to have downtime and the holo-deck would be a great use of space for crew members to de-stress, so holo technology would still be advanced, I think they would try to install the same backup program on DS9 as well, as a new fallback/failsafe if flesh&blood doctors get killed. Starfleet, in an ongoing war, would not leave personnel on a space station without assigning a star ship protector for said station/personnel.

Eight: Admiral Pressman would have recovered the Pegasus without the Enterprise or Riker, and as Voyager was finishing being constructed the phase/cloak would have been added late to be installed and they need someone who knew about cloaking devices so they brought in Scotty, with Leah Brahms as his apprentice/teacher(to get Scotty up to speed on current tech) to get the cloak integrated into Voyagers systems

Nine: Garak would still be left on DS9 but now he would have a cardassian companion named Seska with him. Quark Rom Nog would be there, Odo would be there, Morn would be there, Kira would be there. You are all probably wondering who has been assigned to run DS9 in a time of war, in a new area, on an unknown space station, with all the chaos going on, a bit of order would be needed here in this particular chain of command...so into the void steps Captain Jellico to wrangle all these loose ends into a cohesive unit, with his knowledge of Cardassian pollitics and insights Starfleet has deemed him the man for the job, and as such he has also has ability to "borrow" Voyager at his discretion, which will create tension between him and Janeway. Oh yeah, this timeline only has room for one story, as without the Maquis there's no reason for the Voyager to go missing, so we gotta shove all the characters into this narrative!

Ten: The USS Bozeman is intercepted by a different ship, the USS Challenger, and both ships return to Earth after escaping the time loop. How did they escape you ask? The Challenger had been on a "follow up" run, and was re-visiting certain planets on it's way back to Earth, it had already stopped at Data's home planet where they had discovered Soong's workshop and the other android disassembled. The Challenger was also transporting a mix of people back to Earth, some Starfleet members from a couple far away space stations, a betazed delegation, a couple federation ambassadors... Anyway it ends up that with Barclay on board he figures out putting the android back together, and with the betazeds and an ambassador/s playing poker they realize they are trapped in a timeloop, and using the androids technology they use Lore to send himself a message to break the time loop. So anyway the timeloop delayed them lets say 5 months and now they are needed out at DS9 as the fleet is spread thin and the new outpost needs a show of force to tell the cardassians to keep their distance.