Doc's disappearance's odd. Not just because it's fast, but notice that before they return to the 80's Doc isn't disappearing. His movie ticket is fading off; he's not. Also, why would Einstein have disappeared as well? What i'm trying to say is i don't think any of them has disappeared at all. Why they're not into the Delorean beats me though. I have a wild theory and a silly theory.
The wild one is that Marty and Doc got separated in the middle of the time travel, the Delorean has divided and the other version of it took Doc and Einstein to another timeline or left them in the 30's. This would have happened because of Marty trying to brake the car just while they were crossing the time veil, for example. It's weird all right, but have you seen what this guys have done with time travelling in Sam & Max? This ain't gonna get half as bizarre as in Sam & Max, and now that i think of it i don't even know if there are the same writers involved, but Telltale has a way of doing in cool and unexpected ways what has never been done before in a series (like, say, dramatic scenes in Monkey Island)
The silly theory would be that they fell off the Delorean in the crash, and it's a red herring. Say what you will, but to me any of these two options seem more probable than Doc and Einstein just disappearing.
One last thing. Did you see that "CARL SAGAN KILLED" headline on the back of the newspaper last time Doc looked at it?
Hey, i've just noticed the 4th chapter's called "double visions" and has Doc's face on it. Interesting

I don't know if i've hit the nail or not with the theory of the Delorean getting divided, but i'm sure they're gonna give us some serious paradoxical shit and i'm looking forward to it.