The descriptions says it all really -
On this site I'm working on atm, I've changed the com_user component so that when people register, then their username is just the same as their email address ( I think this simplifies things a lot, they're never prompted for creating a username ).
Anyways, I have jfbconnect on another of my sites and I'd like to implement it on this one and I was wondering if you can foresee any implications with me making the very few modifications necessary to set the username to be the persons email address instead of the few options that jfbconnect offers
One of the options for the automatic user creation of JFBConnect is 'email address', so you shouldn't have any issues there. Just make sure you change that setting in JFBConnect to 'email address', and you should be fine.
If you have any other questions, just let us know.