I have toyed with the same question for a 30' boat. The issue that I see is the gross combined weight of your setup once everything is together. A lot of flatbed trailers weigh 5000+ lbs and by the time you add the boat and cradle you will be pushing the weight rating of the truck/trailer/or combo. There was another thread on here about how a boat's rated displacement relates to its actual displacement even dry.
All of the other challenges can be dealt with unless your boat has a very tall cabin structure or a very deep keel. Getting a cradle on and off a trailer isn't that bad as long as it is very sturdy.
I assume you are insured for this sort of thing?