Autotune isn't 100% accurate. It will go in and make minor adjustments, but you still have to read the CLP's with the laptop, and then push them back into the module before they take effect. Then the process can be started again.
You'll need '09 headers, or you'll need to have bungs welded in, as the TM still uses the 18mm O2 sensors, and '10 and up uses 12mm sensors. You also lose the factory ETIMS with the TM, as the entire computer is replaced.
But, here's my story.
I installed TM with AT on my Dyna back in '08, along with pipes and a/c. Ran pretty good, but fuel mileage wasn't very good. In '09, I did a 107" with a fat cat. I could NEVER get the TM to work with that build. Even TM couldn't come up with a tune that would work. So, on the advice of a reputable mech, I installed the TTS. WOW!!! What a difference in power and fuel mileage! I never got better than 38 with the TM, the TTS is never less than 43, and on open highway, 48-50. Colorado was 58 mpg this summer! I also felt the TTS is easier to use.
I just picked up a Roadglide a couple weeks ago. It came with V&H dresser duals and cans, a/c, and the TM with AT. It seems TM may have made some improvements in the software and other things, as this one runs better than I expected. Mileage is still iffy, at about 40, and she still seems to run pretty warm on those hot days, but I think that is the nature of the bike.
When I found out the bike had the TM installed, it took me about 5 hours and a few calls with the dealership looking for the stock parts before I agreed to purchase. That's how unsure I am with the TM.
I'm very tempted to buy another set of headers and the TTS just to try. With my previous experience, the TM is better, but I still don't think it's all that and a bag of chips.
Long and the short? If I had been buying a tuner, it would have been the TTS, hands down, never even thinking twice or looking for something else. But, since the bike came with the TM, I'll give it a try again, but if it throws fits, it's gone!
Good luck in your decision!