Their not a significant costs difference between E-Tune vs. ProTuning. The quality of the E-Tune is completely dependent on your ability to read/take good logs & effectively communicate with the the tuner. The ProTune luckily will have the tuner in person taking the logs & if there's something you don't like (after some road testing), it can quickly be addressed.
I personally felt more comfortable getting a local tune -- I drove a little over 3 hrs to have Jake from ProTuning Freaks tune my car in person for 93 octane & E85 custom maps. I felt more comfortable with him in the car & communicating him what my concerns are, the specific adjustments he was making to the tune & what I liked/disliked with the way the tune felt.
Regardless of who you go with, I can promise you that a quality tuning experience can be just as important as a quality tune.