As SFDebris points out, Tom Paris is astonishingly competent. Starfleet could want to keep him around for certain, along with Seven and the Doctor. The rest can be sent off on some pointless mission, but Tom, Seven and the Doctor can be their own crazy-awesome R&D department.
Which could lead nicely to that "Apollo 13" idea of mine, have them design and test something new and amazing, and tell what happens. It would be interesting, IMO, to have a new Trek film that doesn't have a villain. Because it's doable, and it fits the whole ST ethos - they aren't out there to fight evil, or defeat the alien enemy/renegade Admiral/whatever of the week, but to explore. To learn new things.
Tom, Seven, the EMH and some peripheral help from the Voyager crew could do this. Throw Barcaly into the mix as well to complete his character arc. And it could be amazing.
To illustrate: Three of the best TNG episodes that I can think of don't really have villains, they're about learning, exploration and the triumph of humanity's better nature, specifically "The Inner Light," "Tapestry" and "All Good Things..." though I accept that the last one is marginal as far as the "no villain" goes. Add in Voyager examples like "Life Line" or (arguably) "Living Witness." Add in "The Nth Degree" for bonus points. And I'm sure there are DS9 "no villain" episodes that stand up very well too, just none spring to mind.
Baltar: "I don't want to miss a moment of the last Battlestar's destruction!"
Centurion: "Sir, I really think you should look at the other Battlestar."
Baltar: "What are you babbling about other...it's impossible!"
Centurion: "No. It is a Battlestar."
Corrax Entry 7:17: So you walk eternally through the shadow realms, standing against evil where all others falter. May your thirst for retribution never quench, may the blood on your sword never dry, and may we never need you again.