I have not compared transmissions.
I always understood that each change with engine, transmission, and chassis, is an improvement over the previous versions. Every version is very reliable with one exception with the engine pre-2005 or pre-2004 where the later version addressed spark plugs popping out. Outside of that particular change to address reliability, each change improves driveability, performance and/or fuel economy.
There is nothing wrong with the transmission that preceded the 2006 TorqShift transmission. The TorqShift is a tad bit better as are the transmissions that followed after it.
We have a 2007 E350 chassis with V10 engine and TorqShift transmission. Simply said, it works great in all circumstances except one. My only complaint is that it down-shifts too dramatically when the cruise control is on while climbing over-passes on the interstates. There are enough gears, but the software programming of when to shift and what gear to select, could have been better for our particular rig with tow vehicle. But each motor home is different. Maybe it works better for bigger/heavier rigs towing more.
One item in our 2007 TorqShift transmission that Ford discontinued in later years is that we have an additional external bell jar style transmission oil filter. The internal cartridge resembles a roll of toilet paper. I think the 2006 also has it. It seems good to have for extra filtering and also extra cooling. Ford discontinued it after 2007, I assume they considered it excessive protection and discontinued it to cut cost. I wonder if the external filter setup dates back further.
Here is a picture I found on the web....it is not my rig, but the filter arrangement resembles mine.
Here is a picture of the cartridge.