I would like to see more checks against the Federal government by the States. We had a good measure of that before the 17th Amendment, and the Senate should once again be chosen by State legislatures. Why do we need two chambers of the legislature chosen by popular vote? It's redundant. The Senate was meant to represent the States.
I also think we need to do something about the Supreme Court. Just brainstorming here, but maybe have the Court periodically (every certain number of years) reconstituted entirely, and effectively on a rotating basis among the States. So if we have nine justices, every 10 years or so nine states will fill those slots with either an appointee or a member of their own state supreme court.
Of course, simply getting the Senate back to its intended role as the States' representatives would fix most of this.