I have a feeling that JJ is playing with us.
I honestly didn't pay attention to the opening credits except to notice that it was better than "the many aliases of Sydney" as AOIIalum put it.
I think if Michael Vartan is still there than it would only be wise to take him out of the credits until they intend to "show" him again.
Plus, the TV Guide (newest one) reported that JJ wouldn't say 100% that Vaughn is dead. So I tend to think he is alive but in hiding.
We shall see