You have a very bizarre use case scenario. Buying two of the same system seems kind of crazy.
As for the console of choice, I wouldn't let the controller deter you. I started with a preference for the DS3, then switched to a 360 controller without any problem, and I'm looking forward to getting my hands on the DS4. My fiance did the same (Though she still prefers the DS3). We both have since been playing the Wii U a fair bit and adapted to that controller setup without issue. You're going to adapt regardless of the controller if you're at all adept at playing games, so don't let that be a deciding factor. I don't know how willing or able your wife is in regard to this, but if my fiance is anything to go by, she was hesitant up front about using a different controller and ended up having zero issues (She's also looking forward to the DS4).
As for the consoles themselves, if you're buying two, $200 savings on getting PS4s seems like a big benefit. When it comes to the games, I'd be absolutely floored if BF4 wasn't equal to or better in terms of performance on the PS4. (If it isn't there's evidently "secret sauce" we continue to know nothing about or the programers for the game are shit.) I think that will likely be the case for all 3rd party titles this gen, just like it was with the 360 in the last gen.
When it comes to exclusives, that's obviously something you've got to decide. Long term, it's hard to know who will make what, pay for what, or how timed exclusives will play out. I wouldn't invest too much into the launch lineup as a result. Consider the longterm franchises and how much you're willing to bet they'll still be good going forward.
I'm a PS4 on day one, but the choice was easy for me. While I didn't expect to have come to that conclusion before this year, the PS4 just looks like a better machine, and since I want nothing to do with Kinect anymore and PS+ has effectively made me feel like an idiot for paying for Live, Sony's getting my money. You've go to choose the one that's right for you though.
