Unfortunately you will be stuck with the software once you pick which unit you want. Stratus and ForeFlight only work with each other. Neither supports alternatives for the other half of the system. There's a rumor about Dual support for Foreflight, but I'm not sure when that will happen. The same applies to Garmin Pilot and the GDL39 combination.
WingX Pro supports the largest number of receivers, but once you pick one of those, you'll probably have to stay with WingX Pro to keep using it. I happen to like WingXPro the best of the three most popular apps, so when I decide to pull the trigger, I'll get a receiver supported by WingX.
In any case, even though the receiver is the most expensive part of the package, the software is what you really use all the time. I'd probably pick the software I liked best and buy a receiver supported by it. At this time, I'd also prefer a receiver with AHRS built in to enable backup gyroscopic instruments on my iPad.