As also mentioned elsewhere, the Nexus S — which is included in Apple's suit — is completely stock Android as far as I know, so Samsung's modifications seem to be irrelevant to Apple's beef with the phones.
Yeah, there there's too much of a difference (IMO), especially as the device itself looks substantially different. Android, I think, looks plenty different to avoid the suit - the Galaxy S in particular, though, doesn't. Not sure what their aim is there.