DT -
The answer is simple. Vito made American Airlines and offer that they couldn't refuse!

Seriously though, you make some excellent points.
We know that everything has to be done very quickly because Johnny tells Vito : "It's too late, they start shooting in a week."
As for Michael taking the train instead of a plane in GFII, I believe that it was Turnbull who pointed out that Michael probably wanted to travel incognito because someone was trying to kill him, and therefore found it easier to do so by train than traveling on a plane.