Aside from that, he or she can issue Executive Orders, which "have significant influence over the internal affairs of government, deciding how and to what degree legislation will be enforced, dealing with emergencies, waging wars, and in general fine-tuning policy choices in the implementation of broad statutes."
Except that when those orders go to far against the wishes of the permanent government, the orders get blocked by the courts.
The issue is that it takes virtual all of a president's political capital to fight the permanent government (the bureaucracy, the courts, academia, the credentialed media, the party apparatus). So while in theory they have quite a bit of authority, if they wish to use that authority in a way that goes against the interests of the permanent government, they will find themselves in a huge battle. They can win at most, maybe one or two of these battles a term, and only these in a limited way.