The two auto transmissions are very different. The one behind the 5. 9 is the 48re 4 sp auto which pretty much dates back to the Chrysler 727 from the 60's with obvious updates along the way. The 6 sp auto behind the 6. 7 is a much more state of the art piece and features things like shift control buttons on the shifter to pick your gears if you like.
The 6. 7 has a rediculous amount of emissions controls on it. Have you looked underneath both to compare? There is a lot of extra junk on the 6. 7.
If you need/want an auto, the choice is tough. If you were considering a manual I would go 5. 9 all the way. The emissions system on the 6. 7 concerns me, lots of complexity, lots of computer power relied upon to make it function well. The new trans is defiantely much better, the new turbo with integrated exhaust brake is also much better (more effective). This seems typical in most new vehicles that as features, functions and controls are added, the amount of processor power is increased.
So you are either in the "keep it simple" camp, or in the "latest and greatest" camp. Both are likely to be great trucks. Most of the bugs seem to already be worked out of the new trucks. Seeing all this technology coming down the pike though, I personally opted for a 5. 9 six speed. Some thing I plan to keep for quite a while, and I appreciate its relative simplicity. Of course by that notion, I should have bought a '92 first gen twelve valve:-laf So there are compromises along the way depending on what you want/need, and the level of complexity in a vehicle you want vs. the features.