I would LOVE to see Hillary prosecuted, but I don't think that is where the most mileage is to be had. Go after all those AROUND Hillary. Any one who paid into or received fund from the Clinton Foundation. Put them under the financial / RICO microscope. Freeze their funds if any wrong doing is found. The Clinton's are toast. Both are too old to hold office again. But if you go after their cronies, you can severely damage the liberal "bench".
Then, once you have any Clinton Dem who dares to raise their head afraid of the smack down, finish off Clinton with at least an impeachment with a denying of any further office and any pension. Jail time would be nice if possible.
I still think that Congress should use it's authority to create tribunals and courts lesser than SCOTUS to create a means where Congress can refer senior officers of the government for prosecution - even if the DOJ does not.
I think you will see changes similar to the ones you describe under Trump. The Founding Fathers and most ordinary Americans always simply expected that government officials especially at the highest levels of office would behave with honor. The only best things about the Obama term in office is that it has taught America how to deal with an anti-American, contemptuous, President.
No one ever expected the DoJ to be completely incorporated into the Presidential staff, the way Obama did it. And no one ever expected the IRS to be weaponized and turned into a personal Gestapo unit of the President, the way Obama did it. It would be normal for Congress to learn from these examples and to set up safe-guards to keep it from happening again, under any President.
If the DoJ becomes as thoroughly corrupted as it is today in the future, it seems normal that Congress would pass some legislation to be able to get around it. Otherwise, as we see today, the legal checks and balances on members of government disappears.
There has already been talk of making the Attorney General an appointment of Congress instead of being a direct appointment of the President. I don't know why the system was setup this way. Because having the Attorney General appointed directly by the President, as we have clearly seen for eight years, can lead to serious conflicts of interests and an utter corruption of the rule of law.