Pushers are generally considered better buses. Better weight distribution, less noise up front, less fumes up front, shorter rear overhang (less scraping on the ground), easier to work on the engine. One possible drawback is weak air flow to the radiator, but I believe that any overheating problem is primarily a matter of cooling system maintenance.
The front engine design has one key advantage: You can have a door in the rear. That's the one reason I have mine. But a front engine will give you noise and fumes in the bus, and the engine is difficult to access. And you have to climb over the engine cover to get in and out of the driver's seat. And you have a drive shaft under the middle of the bus, taking up space you might want for water tanks and such. Front engine buses always have long rear overhangs, presumably to make the drive shaft as short as possible.
The engines you mention are both good, with the IH preferable. Allisons are OK, and pretty much the only game in town, unless you stumble across a manual tranny. The Allison AT545 is most common, but the MT643 is preferable. Typically, you will find the big tranny in the biggest buses.
Price and availability will be a factor. Those front engine flat fronts had their glory days a decade or two ago and are readily available. These days, most new school buses are pushers.
Does that help any?