I run SERT and SEPRT (or what ever its called). My tuner is happy with both but the TTS does offer a few extras and if I were to go again thats the way I'd go. If your tuner is any good he wont need any 'start up' maps. He'll just redo them anyway.
If you go SERT or SEPRT, don't rely on a dealer flash download as the final tune. Find a tuner, a reputable one and talk to him (or her), talk shit to find out what they've worked on and what they'll do. Work with them to get the best option for you. The tuner has to be happy and confident with what they are working with. In short if the tuner can tune they can work with SERT, TTS ThunderMax and make all of them as good as they can be for you and how you want your set up.
Now we are talking Harleys here. Dyno's will give you the best result (and a pretty print out to brag about) but my tuner plugs in his data collecter goes for a few rides and works off the print outs, he sets up a riding tune. Cheaper, gives me about 95% of what a dyno will, I'm happy. You want a race bike go dynor, you want a street bike then a data collector in the hands of a good tuner will work just fine.
Now thats only my opinion. Take it for what you will, all depends on how good your tuner is and what gear combo your running.