Madison and a number of others had a very strong confidence in the executive branch, that in my opinion was based on lack of foresight. Their primary experience with executive power came from the English king. They assumed that the legislative and executive branches would always be natural enemies, because the king and parliament were constantly at odds with each other, with the latter having the sympathies of the people. What they failed to keep in mind was that this was because in England, the two branches derived their power from very different sources. But when the executive is elected, then he becomes the favorite of the people, and the legislature becomes relegated to the sidelines. This is a development which I don't think they anticipated at all.
A big difference from then and now is the change to popularly elected Senators.