This was an easy decision for me since I have a transit without the room underneath. I do not have engine run dash air (did not want to run 40ft of freon line). So I have three Coleman 13,500btu with standard hang down diffusers (not ducted). Front A/C is mounted close to the front, and with a dash fan, I stay very comfortable, even in 100 degree weather. The second is just about in the middle and the rear is over the bed. Going down the road usually run the front and back, with the middle used at night. While the Colemans are good units (don't get the heat strips-are about useless), they only have a two speed fan which is more like high and medium so night time use is not as quiet as I'd like. The Duotherms have three speed fan and I understand the Carriers are quiet-with Carrier also having the lowest profile unit available. Advantages- easy to install, easy to service, about half to one third the cost of basement units, can replace one in about two hours, most every RV supply house has them in stock, very proven. Dissadvantages-have that weight (in my case about 300lb) high up on the roof, you have the not so good looking units on the roof to look at, more likely to leak.
As far as basement units, there is the split type with the condenser and compressor underneath with the evaporator easily placed (relatively small) inside a cabinet. Most noteable type is Cruiseair by Duotherm. Then there is the split type that has just the condenser outside with the compressor and evaporator inside. Mount on the floor and duct it up to the ceiling for discharge. Relatively easy to install, are quiet, but cost about 3 times a roof mount. Then there are the all in one units where the condensor, compressor and evaporator is all underneath in one cabinet. This is usually the most challenging in that the design and sizing of the duct work coming up into the bus is critical. Also expensive.
Personally, if I were to do it again, I would use the Tundra split system that has been built for the trucking industry (www.tundra.cc
go to trucking).
You'll find all sorts of opinions here. If you are in doubt, the roof top is always the easiest, and also keeps all that equipment out of the basement. Good Luck, TomC