My daily commute is about 5.5 miles of suburban driving maxing out at about 45-50 mph and my oil and coolant gets up to temp in that driving. The transmission doesn't fully warm up but I doubt that's a big deal. I do get out for longer drives too of course, but not every day by any means. From what I've read these trucks don't have nearly the trouble with emissions on shorter commutes as the older pre-DEF trucks. You may have an issue here or there with emissions, but as far as I'm concerned there aren't any motors out there more reliable than a Cummins over the long haul.
Don't settle for gas if diesel is what you want - the CTD is an awesome expereience and if you settle you'll never be satisfied. Also, have you actually driven them back to back? They're quite different and I knew once I drove the 6.4 that I wouldn't be happy without that straight six under the hood.
As far as Aisin vs 68RFE, I've been happy with my 68 and I think it shifts well. Most of the failures you hear about on them involve tuned trucks. If you keep it stock it's a very reliable transmission.
