First, I didn't agree with the call, but I don't think it was as bad as some sportswriter geniuses think.
Two options:
2nd down: run (Patriots "know" it's coming)
Timeout Seattle
3rd down: pass (Patriots know it's coming)
4th down: run or pass (Patriots guessing)
2nd down: pass (Patriots don't see it coming (other than DB's, who are playing pass first))
Still have timeout if incomplete
3rd down: run or pass (Patriots guessing)
4th down: run or pass (Patriots guessing)
If the coaching staff is thinking of a 3 play series (after 1st down), it makes sense (I still don't agree with it, but they know more than me). Either way, you get a maximum of 2 runs.
I, nor anyone else, know what would have happened on a 2nd down run. A run blitz could have caught them in the backfield. An incomplete pass on 2nd down makes the Pats play a little more safe, because of the run/pass/option/roll out possibilities, making it a much easier score.
Again, I don't agree with the play call, because I think you have to do what you do best (led league in rushing), but having coached FB for ~20 years (and baseball and basketball), I tend to give the coaches more of a pass than most.