I would definitely go with Cobb and EQT.I've always had very good results with APR, have been stage 1 on two R's. I have not gone stage 2, stage 1 always just seemed like enough. It is unfortunate that stage 2 with APR is going away, and this makes me second guess going stage 1 on my new R with them. I still may never go stage 2, but I might, and I'd hate to have to switch and go with a different tuner if that was the case.
I've heard great things about EQT (works through the Cobb AP), both in terms of customer service as well as power (seems to be on par with APR, at least for stage 1). I may go this route this time for a couple of reasons, can sell the AP in the future and recoup some of the spend (not necessary, but still something to keep in mind), and they should continue to offer a stage 2 solution (at least it seems so for now) if I decide to go that route in the future.
The flashing "at home" option is nice, and APR is missing a bit of market share by not having this so far, but I've heard they are developing a product for this. If so, I would assume that it will be out soon.