I have to echo the ideas on Voyager building a new vast alliance with various other races. Not only does it make for several intriguing arcs, it made for a fitting reversal to the other Trek. The threat of the Gamma Quadrant threatens to destroy the Federation on DS9 while the hopes of the of the Delta Quadrant will potentially allow it to be reborn thanks to Voyager.
In addition, perhaps the nature of the Maquis goes beyond just a willingness to bend the rules, but maybe a real schism in the citizens of the Federation. Make the agreement over the DMZ more of the straw that broke the camel's back with some of the Maquis showing resentment for the Prime Directive, Starfleet's noninterference in the Cardassian Occupation, etc.
Hence the building of this proto-Federation also has conflict between the traditional Starfleet officers, the radical Maquis members, and the various Delta Quadrant species. As a result of this input, the final alliance embodies much of the spirit of the UFP but in many ways is a much different beast.
Definitely make Janeway a largely untested officer initially way out of her element, but gradually growing and adapting over the years. The relationship between her and Chatokay is more of a partnership at first, with the two practically being co-captains given Chakotay's vast field experience in comparison to her. Over time she gets more confident and he defers to here authority more and more.
The ship does end up home in the sixth season finale, but it comes about specifically because of their work in creating an alliance in the Delta Quadrant. The last year of the show are devoted to the crew's reaction to what's happened back home (the Borg incursion, the Dominion War, how Starfleet has changed) and the eventual encounter of the Federations in both the Alpha and Gamma quadrants.
Character bits:
-The Doctor is largely the same, though he pursues romantic relationships earlier than he does in original canon.
-Tuvok is initially a by the book Vulcan and Starfleet officer, who gets more emotional (and hotheaded) as the years go by and the lack of contact with other Vulcans starts to affect him. He is the biggest opposition against the Maquis at first, being fairly distant and aloof dealing with them.
-Paris remains a major black sheep to the Federation and Maquis officer (even though he is a technical member the latter) for a long time, largely because he remains remarkably cynical towards the ideals of both groups. Initially out for himself, his relationships with those from the two sides (Kim and Torres) eventually softens his rougher edges.
-Neelix is a very old and eccentric figure, someone who's seen it all and done it all in the Delta Quadrant. His own personal interests and goals are so very different from the crew's, with his own biases occasionally playing a part as a liaison and guide. Eventually the crew does find some common ground with him.
-Kim is wet behind the ears idealist, initially looking up to Tuvok. An unlikely friendship with Paris and the difficult years in building a new Federation affect him deeply, and he struggles with his Starfleet principles vs the contrasting reality around him. While emotionally vulnerable at points, with his skills he turns into an efficient jack of all trades on the ship, working in several different departments. He is often a secondary character.
-Kes is a traumatized refugee rescued by the crew after they're stranded who's attraction to the concept like the Federation leads to her being gradually trained as a Starfleet officer on the ship and her involvement in the alliance building for the proto-Federation. She has a romance with Kim for some time.
-Torres is half-Romulan as opposed to half-Klingon, and is the more calculating, pragmatic Maquis in contrast to the emotionally driven Chakotay. While still in engineering, much of her role is as a leading planner and designer of the proto-Federation. She is the only initial friend to Tom Paris at the beginning, which grows into a romance eventually.
