I updated my iPad 4 running stock 6.0.1 to 6.1 and i haven't noticed any changes.
If you don't want to run into any possible complications, i would suggest that you simply update via Wi-Fi using the OTA (Over The Air) update. Just go to the Settings app and update from there.
If you want to do a complete restore by wiping all your data and installing iOS 6.1 as stock version, then you might be in some for trouble, unless you have some experience. Here's a guide (more of a troubleshooting process) on how i managed to do it: iPad bricked? Restore process errors!
According to Apple, changes in iOS 6.1 include: