If *I* had a 'time machine', (...and an 'in' to Paramount Television Productions (*Grin*)...)
Take the basic premise...and extend it.
Two crews, one ship, 'unfriendly' territory for both. (Both within the ship and without, given the circumstances.)
Balance 'interior' versus 'exterior' danger - that is to say, inversely proportional, but with enough variation to keep suspense. Some episodes, focus on the interior 'rivalry' between the THREE factions - 'hard core' Starfleet, 'hard core' maquis, and the 'realists' who forgo previous alliances in favor of continued survival - call them the 'opportunists'...
(...also 'in play', but not revealed until much later - the 'fourth column' - a VERY FEW from each crew where idealism overrides any other previous commitment. Built up, slowly, when they 'go against type' in the defense of certain ideals...)
Other episodes, deal with almost solely 'exterior' threats... with an eye to how the interior division increases the danger, but that same diversity provides solutions that any single group wouldn't have come up with...
The ship herself is first 'idolized' by the Starfleet crew, hated by the Maquis... by second season, (almost) everybody hates her, all the work and trouble - the ship herself begins to look 'run down'... (Forshadowing: The 'idealists' are shown to SAY they 'hate' Voyager, yet their actions differ...)
By third season, the ship herself takes on a personality - BECUASE of what she's survived with the crew, rather than BECUASE of it, she become 'anthropomorphic' - is given a 'personality' in the minds of her crew. Certain members get special treatment, showing how they go out-of-the-way to keep Voyager in ship... indeed, a few speial 'lower deck' episodes show incredble lengths, that are 'brushed off' by the caracter themselves.
(Harry risks life and limb in an episode that shows he should get the Trek-equivelent of the Medal of Honor... yet, handing the part to Tuvok and unable to expalin the risks he took 'logically', shrugs it off as 'no big deal... (with the in-story 'double-take' being that Tuvok had been investigating a possible security breach, and by the time the part is handed to him, knows just what lenghts Kim went to in order to get it...)
Extend upon the intergration of the crew - i.e., the more they come to know them, the more 'human' they seem. (*This includes 7 and the EMH, but in a less 'forced' version... and the ship, in a MORE 'forced' version, matching reality. Ask any 'old Navy man' about his ship... *Grin*)
Final episode...? Everything is against them, and 'rational' decion would be to fragment and 'take the best deal' for each group... the fact that previously-hated aspects, including the ship herself, are threatened, instead of addding to the urge to 'defect', boomerang and stregthen the desire to resist - then the few 'idealists' attack. Not out of hope of winning, but just becuase 'certain battles are worth fighting'... and it's enough to rouse the entire crew to fight.
The battle rages back and forth over a four-episode arc, until it seems that the failure of the crew by a slim margin is yet nevertheless certain... and then have the crew saved to get home by that one, last hold-out 'opportunist'... who, having 'hijacked' the Voyager, comes racing in to save the day, revealing himself to have become so sucessful at hising his 'idealistc' nature that he'd even managed to fool HIMSELF... until the last minute, of course.
Final episode...? After getting home, the hidden idealist, as punishment, is 'forced' to basically rebuild the nearly-destroyed Voyager from the keel-up... but, having one the 'Federation's Highest Decoration for Bravery' in that last action, is basically given carte-blanc to do exactly as what he/she wanted to do in the first place, but had been deluding himself all along...
Last scene, the remaining crew to see the new 'Voyager' about to be sent out on her first crew... fade to black just before the reveal, with the presumption of a sequal series.
...but, hey, that's just me.
XI COUNTDOWN CLOCK: