Just making sure, I can still use Permissions 3.x? I don't need to use the bukkit incorporated one? Automatic converters for Permissions 2.7 and 3.x are on their way, but in the meantime you can still convert your configurations manually. It says you "can" convert them manually. Does that mean I have to? Can I use Permissions 3 and leave the permissions.yml blank?
You don't have to use it. Some plugins are staying, some are switching. Once (and hopefully) groups are implemented, the permission plugins will begin to fade.
So why did bukkit add their own permissions? To me it seems like changing from Permissions 3.x to BukkitPermissions is a hassle.