I honestly have only tried the quick tunes on both the 87 and 93 Octane tune(s). I haven't tried using the advanced tune yet since I'm barely into my 3rd tank since running the 3872 Flashpaq.
The shift points as well as the mileage hasn't really changed, if at all. I will say I have been stomping on the gas pedal more since the throttle lag isn't there anymore (which I like for obvious reasons). I'm going to give the mileage tune a try once I get back to my office on Tuesday since that was where I left my tuner.
Really, with the quick tune, it did a great job wakening up the ol' JK. Like I said with the 87 Octune tune, it was certainly a noticeable difference in power delivery and responsiveness. It really should have came this way from factory!
If you're on the fence about picking the new Flashpaq I would say go for it. Best $300 performance mod you'd make!