I can buy that the train driver didn't immediately finger him as the train hijacker (how many long silver haired old gentlemen with a suspicious interest in trains has he met?). Okay, I can buy that given time Doc could design a locomotive that doesn't shred itself going to 88 MPH.
So basically, how did Doc build a time machine in the 1880s? His one explanation 'It runs on STEEEEAAAM!' explains exactly nothing other than how it can run so fast. But this last one right at the end annoys me, and it makes me glad the game chose a duplicate Delorean over this atrocity of steam and tears.
So like everyone else I watched the trilogy recently, and despite what people say about plot holes I think most of it is solid and holds up well.