It will all stay the same basically as they will still be the same company under the table.
If some tosser decides to take you for a ride ebay will still grab money out of your paypal just as quick as they do now.
I'm pretty sure ebay wont be going back to how they used to be when they allowed you to put various other payment options on your listing, like nochex, worldpay, pppay, sagepay, or one of several dozen others. They took all other options off just before they annouced they had bought paypal. You can still take whatever method you want but you have to sort it with the buyer directly instead of having the payment buttons directly on your listing, as other sites still do.
The biggest problem with ebay & paypal is they are so big that no one will use other sites like ebid, CQout, Ioffer etc.. so ether you sell/buy on ebay or don't bother, and ether you take paypal or don't bother.