This is something I've been thinking about a while now. With the BTTF3 ending, the story is completely closed. The doc takes his family on the train, and leaves. The delorean is destroyed, Marty goes off to continue regular life. Maybe he'll see doc again, maybe not for quite a while. Not a bad ending.
With the BTTF:Game ending, marty and doc go off together. You get the feeling they'll be having these fun adventures for the rest of their lives. The delorean is still around. The timeline has obviously got problems, but they realize that their present selves and their friendship is all that really matters. I loved it.
It basically comes down to this: I think it's better to close the story focusing on Doc & Marty, rather than Doc's family and the timeline. It's really a testament to the game's writers that they made something that not only stands up to the trilogy, but actually improves on it.
Just some thoughts for you fellow BTTF fans out there. Would love to hear your responses