I've played the closed alpha and a good bit of the scale tests with a fair number of xbox players I've met through the game. Really the only issue I've encountered is that it's a bit trickier to add players to your friends list via the xbox PC app.
I recall one time when I was playing with a friend of mine, we docked at an outpost and another duo crew showed up and asked if we wanted to fleet up. I suggested we add each other, back out, and queue as a 4 man crew. Since they were on console, I had to ask them to add/invite us etc. to accomplish all this. It worked out quite well, actually, but I digress.
I see guys debating the whole kb/m vs controller thing a lot, and really it all comes down to preference. I know a couple PC users who use their controller for some games, doesn't hamper them any. Just as well I know some pretty good console players who don't seem to be at any disadvantage only using a controller.
Cross Play is fine for this game. I've not had any negative experiences that were really noteworthy come about because someone was or was not on console (aside from the aforementioned xbox app thing.. which is in itself a POS). Although, maybe I lucked out? Who knows. Regardless, separating the playerbase by offering a means to filter out either side of it would, in my opinion, hamper the game a bit. Nobody wants a huge divide in their game's players. Unless they add Ninjas or something, THEN it's time to take sides.