I checked into the Marriott, they gave me one limited edition key and the rest regular keys
I also checked into the Fairmont, they gave me all limited edition keys
The only problem is that I can't tell which keys are for which, they should at least had the hotel's logo on those keys
That's weird. Each hotel was supposed to give out the FanimeCon keys during check in and normal keys after that (for reprints, etc.).

I'm not sure that not having the hotel logo on the keys would have been a major issue since I don't think many people have access to multiple hotel rooms. I know that I was given a key or two to other staff members hotel rooms and I just marked the keycard appropriately.
Cards like that are cheap. Even cheaper in bulk. Fanime no doubt just got several thousand magnetic swipe cards printed when they got the pre reg and staff badges printed, then handed the blank cards out to the hotels Fanime had contracts with.
These hotel key cards were printed independently of the Pre-Reg and Staff badges.

This is the first year Fanime did the souvenir hotel keys. I believe there were 5 images. All of this is courtesy of the Marketing Division. 
5 total images with 2 different sizes (one for Hilton, one for the rest).
Also, I'm glad that we were able to bring this to you folks (the members). I was really excited when I first got the proof and it was a really nice surprise that not most of our staff didn't know about.

Will this happen next year? Maybe. XD