I'm going to go out on a limb and say that Disney will have policies and procedures in place to handle most situations.
Additionally, I would almost guarantee that there will be overlap and if paper media is ever fully eliminated (which I wouldn't bet on), it won't be for years and years. ATS and various other systems are quite efficient at the moment. For example, when a cast member brings a guest into the park, it prints you out a ticket right at the gate. It'd be much more of a hassle to encode a RFID wristband right there.
If I had to guess, WDW will be entirely RFID by 2015. But it will be a combination of wrist bands for resort guests and cards for day guests. This will have the added benefit of easily being able to identify people staying on property. Not sure about APs. Mike, how long do you think the battery would last?