Dear Rev. Williams,
I am afraid that this is a bit like asking which shoes are best: it depends if you're planning on running, hiking, mucking about in the farmyard, or dancing ballet.
What do you want to do with your bus? You get different answers for full-time living, occasional weekend jaunts, carrying motorcycles to events, or using it as a moving van.
What type of driving will you do? Some buses are geared for city streets and can't get over 55 MPH. Activity buses and some transport buses have highway gearing. Is power important? You'll want the Cummins 8.3 instead of their 5.9, or International's DT466 instead of the 444.
How many miles are you likely to put on it each year? Occasional weekend jaunts, if nearby, might not require highway gearing. Drive once a quarter and park the rest of the time? You might be plenty happy with a low top speed - or rotten miles per gallon, for that matter.
Where will you be going? In my case, I plan to cross the Rockies. Because they don't lock up (providing deceleration), I won't consider an AT 545 transmission. You may be plenty happy with the 545 (CadillacKid is), for instance, but you ought to consider its characteristics. Looking at winter weather? You might be delighted to find a bus with automatic chains.
How much room do you need? Flat front buses have more usable space than does a conventional of the same length. Often you'll see undercarriage storage bays in RE buses, since they don't have a driveshaft to worry about. (You'll often see such storage under other buses as well, of course, but there is more room under a RE bus.)
Are you on the paranoid side so far as safety is concerned? Conventional design puts more metal out in front and would be safer in a collision. And I am not interested in hydraulic brakes - I had them go out in my wife's car and pedal to the floor with no braking effect is... disconcerting. When they fail, hydraulic brakes give no braking power. When air brakes fail, you screech to a halt.
Is price a consideration, as it is for me? Conventional buses are often cheaper. And CAT parts must be purchased from a dealer and can get pricey.
Doing your own work? Conventional design provides the easiest access, and FE the worst (though you're out of the rain). Might need a rebuild? Cummins 8.3 and International DT466 let you do a rebuild with the engine still in the bus, while others (not sure if all or just most) require it to be removed.
Do you have any special considerations? I need to move a piano, so I need the full-sized back-center emergency exit. That would suggest FE or Conventional for me. But I want to put a co-pilot's chair near the driver for my dear wife, which kills the FE option for me (but that's OK because I was head towards conventional for price anyway). Motorcycle transport folks might want a wheelchair lift. Going to the national parks? Might want to stay around 35' for maneuverability. And so on.
This will get folks started: you're likely to see a lively series of contributions to follow.