Um, Disney has a ton of ways to track guests. You have already been tracked just by reserving your resort room. It's the year 2012, you are being tracked every single minute of your day.
But back to Disney World - yes, online check in can save you a lot of time. But it's meant for people who don't have tons of requests and just want to get their room key, basic resort info (without tons of verbal information), and the parking pass. Just show your photo ID and credit card, pick up your packet and go.