In my experience it's pretty hard to get a seamless transition between two wheelsets. You need the rotors and cassette to be in the exact same place which is going to mean you'll need the exact same hubs, and even then, I've found that things still might not exactly line up (that said, my experience is mostly with lower end stuff that probably doesn't have the tightest tolerances). Of course if you're fine with making a few adjustments every time you switch things over then it's no big deal.