We've always done our Powell trips by speed boat until recently. After two trips with record heat and wind/sand storms we've decided it's nice to get a house boat as a barge to carry ice, and gas and to get out of the storms when they roll through. For extended trips, the hard part with a speed boat will be the ice unless you go during a cooler part of the year. During hot months we had to go back to the marina nearly on a daily basis for ice unless you pack like a river trip with frozen meals, dry ice and really good coolers. If you're skiing alot you have to go back almost daily for gas. A coworker of mine does a house boat all the way up the San Juan arm and stays there for two weeks straight, sending a boat back once to resupply.
We've always rented from the Marinas. We've looked into cheaper alternatives and haven't found any yet. Plus boats occasionally break down and it's probably easier to deal with at the marinas. One of the trips I wasn't on, my friends camped with a speed boat up the escalante arm so it can be done, espicially if you aren't skiing (which isn't legal with only two people anyway).
Wag bags and buckets don't count. It has to be an actual portable toilet.
If you're doing exploring, I recommend buying an anchor and rope. The rental boats don't give you much of anything and often there isn't much to tie to except for slickrock. You'd hate for your boat to be gone when you get back. Also, bring your playboats. Alot of the slot canyons are two narrow for speed boats but are fun to explore by kayak and lead to some great hikes.