Both Have Their Advantages
I've used both, but only recently got a canister deep cleaner. What I like about the canister style is that it is much easier to use a wand than to push and pull an upright full of water. The suction is also much better on the canisters as their is more room for a larger motor. What I like about uprights is they are a single unit, so moving one upstairs takes less time than moving a motor unit and hose and then a wand. The extra weight of the water placed on the cleaning head helps pull out more water.
One thing to note is that not many professionals use upright extractors. They either use a large portable or a truck mounted unit, which are all basically canister style. I think the best deep cleaners, consumer grade, would be a Hoover Steamvac as an upright or the Bissell Big Green for the canisters. A professional upright I've heard good things about would be the Steamin' Demon. Almost $5000, but if you have the money, it looks like a better deal than a portable. But I've never used one so I can't say for sure.