CM based ROMs can be more customized into more details. I don't know how it is on Google ROMs because I have never had a Nexus but from what I experienced from CM ROMs that they look more intact, they are raw but I like the rawness.
Another tiny detail is the home screen, Sense's home screen does not rotate.
I don't know if the controls came in Gingerbread as they are not available in the notification field. I know Samsung has had controls in the notification since their ever first releases.
And the fact that Sense is everywhere on the phone makes the feeling that it is a Sense UI not an Android which is sometimes good by the way, like the linking and the dialer.