The biggest reason why Bluebird wouldn't put a manual tranny in the TC2000 FE that I can see is that there is nowhere to put the shifter. Obviously they couls use cables, mechanical linkage, air, etc to attach the shifter to the tranny, just like any other rig where the shifter is remote to the tranny, but the dog house for the engine is right there. Either the shifter would be on the doghouse with linkage making it impossible to open, it would be behind the driver's seat, or it would be on the left side of the driver. Basically, I think it comes down to logistics...it would have teken a lot of engineering to get the manual tranny to work and no one would spec it anyway. Schools figured out a long time ago that automatics are the way to go. The maintenance costs for a school are less with an auto (obviously our conversion driving style is the opposite) and they are more efficient because yes, the automated buses do take off better in stop and go driving. Finally, I think it was a matter of safety. An automatic transmission means there is one less thing for the driver to have to pay attention to so they can focus one getting kids safely to and from home.
Personally, I am a big fan of manual transmissions myself. In fact, the bus is the first automatic transmission I've owned since my 11th grade year of high school when I had a Lebaron coupe. The Lebaron, ironically, died of transaxle failure when it sent a pin flying through the case of the transmission and up through the hood. I was just leisurely cruising at 55mph down the highway.....go figure.
The trend I've seen with the manual transmission in the buses is that they are behind the smaller engines. I think this is to maximize the power available from a 366 gasser say. That's not unlike my Toyota pickup. The 5 speed trucks with a 4 cylinder came with 4.10 gears. If you had the factory 31 inch tire option, it was 4.30's. In the same truck, but with an automatic transmission you would get 4.56's with the 225 series tires or 4.88's with the 31's....and you still got out performed by manual!
As for the big trucks....Allison is actually advertising pretty heavily about their new OTR transmissions claiming better performance and mileage. I can't personally give experience one way or the other, but they do have videos on their site of a true hydraulic automatic spanking both a true manual and the automated manual transmissions in tasks like hillclimbing from a dead stop. There is something to be said for the torque multiplication a torque converter gives you.
I'd like to see the sequential style transmissions seen in some of the German vehicles become more popular in all vehicles. They actually are like two transmission in one. The input from the engine flywheel drives two clutches and two mainshafts All the odd gears are on one side while all the even gears are on the other. When you take off in first, that mainshaft is engaged, but second gear on the other mainshaft is akready preselected such that when you push the clutch pedal (it it even has one...some don't), it engages the other mainshaft instantly. There is not waiting to shift since all the gears are preselected. As it engages second gear, the odd gear mainshaft is now preselecting 3rd gear so that it is instantly ready. It is a need system, but is somewhat complex and would be HUGE to have beefy enough components for something like a medium duty truck application.