It may seem like I am stalking you, Bee, but I am not. Just a time thing here.
Can't remember where exactly I saw it, but under one of the discussions in the bus conversion section I saw someone with a flat-floored full/mid sized bus. Was used for multiple wheelchair transport. Had a ramp out the back, like on a U-Haul truck. only problem was the interior floor was raised to the height of the top of where the wheel wells would have been. So he lost that height overall. It might not be an issue if you are short, but if you are over 5'8 or so, it might matter a bit.
Other people here have found all sorts of creative ways around the wells mucking up their floor plans. I think you are going to be stuck with them, so you might as well design around them.
And, since I live in Gator land, I just gotta say it... GO VOLS!!!!!!!!!!!!!!
(Nothing will turn you off of a certain football team colors than walking into Sears and seeing an orange and blue bathroom display, down to the tub, toilet and yes, the toilet paper. Bleh.)