JFBConnect doesn't use a Javascript popup for registration simply because we have the ability to request additional information from the user during the Facebook registration process. On some sites, this can be 10+ additional form fields. JomSocial's solution is more fixed, which allows them to know how long the registration form will be ahead of time, but not as flexible as JFBConnect. It is a tradeoff. However, the login/register page from JFBConnect can easily be styled however you want. We have classes and divs on just about every element of that page, so you should be able to show, hide, shove, or add color wherever you want.
As for the emails, JFBConnect sends the standard Joomla new user emails. We integrate with a lot of different systems, so we have to send one standard email. If you had profile plugins for CB, Virtuemart, or another system that also sends it's own emails, then users would get multiple new user registration emails, which isn't ideal either.
I haven't tried it yet, but just saw the "Email Beautifier" extension added to the JED. It may help you solve the 2nd problem, if interested in another extension:
extensions.joomla.org/extensions/contact...feedback/email/18463
Hope that helps explain, at least. If you have any further comments or suggestions, we're definitely listening as most of our development comes from user input.
Thanks,
Alex
Layout Registration Page
