I've heard that the Timberwolves want to play more up-tempo, but I'm not sure to what degree. If they plan on running a ton and sacrificing defense (which I doubt they will), then I could see Rubio and Flynn playing together. That would be a very quick backcourt, but it wouldn't work out. Neither player shoots well, they're both inexperienced, and their perimeter defense would be absolutely atrocious. Without a shot blocker in the paint, it would be too easy to score on the Wolves.
A trade is the best option. I'm not sure what they could get in return, but shooting guard is looking like the biggest weak spot on the roster. Small forward isn't great either, and a defensive-minded center to pair with Jefferson is also an option. They will have hands down the worst backcourt in the league next year if they don't make some moves, and having those two together at one position is a waste of talent.
With so many holes throughout their roster, Minnesota is in for a rough season. They don't have the offensive fire power to be anything more than below average, and defense isn't going to be strong either, though Rambis will help in that respect. I predict them to finish in the bottom three of the league (along with New Jersey and Milwaukee). Imagine if they land the first pick and John Wall's the only player worth selecting #1.