Just a ditto about what others have written. My Cannondale R2000 w/ ultegra brakes will handle a 28 tire with the quick release open without deflating. It's a very tight fit, but with a little practice it works fine.
I have my brakes adjusted pretty close, I really don't think they could be adjusted much tighter. When I put the wheel on and off, the tire does rub against the brake pads when I push it through, but it isn't a problem. Loosening the brakes a little would help if one's tire can't make it through. The barrel adjuster on these brakes is so convenient and easy to use that it really wouldn't be a problem to turn it a couple turns putting the wheel on and off. I would definitely try this before deflating and inflating the tire.
I've found that it is important to make sure the axle and dropouts are lined up so the axle slips right into the dropouts when the tire goes through the brake pads. It's hard for me to describe it any better, but if it doesn't pretty much go right into the dropouts when the tire slides through the brake pads, you won't get it. This is only slightly tricky and mastered after one or two tries.
My friend was helping me put on my wheel the other day (I was late and unloading a bike for another guy, and my friend was a little impatient and wanted to help me get going). I was happy for the help, but I noticed he was struggling to get that fat tire on - I had to show him the trick of making sure the axle and dropouts were aligned.
My main source of concern with my particular frame (CAAD7, 54 cm) is that the rear 28 tire is very close to the back surface of the seat tube, and front derailleur bracket on that tube. I think that if I pick up mud or other road debris like mud or sticky fresh asphault sand granules (that really sticks to the tires for a 1/2 mile or so), I'll have to make sure it doesn't cause a problem. If it is, I think I'll switch back to 25's or 23's, but I do like the ride of the 28's.