The Pottermore article on Hatstall includes the following passage:
The only true Hatstalls known personally to Harry Potter were Minerva McGonagall and Peter Pettigrew.
It's obvious that for Peter Pettigrew the Sorting Hat would have been debating between Gryffindor and Slytherin, and ended up choosing Gryffindor.
Professor McGonagall ended up in Gryffindor, so what other House was the Hat trying to decide whether or not to put her in?