In the days of Adams and Jefferson, I'd say the good guys were the anti-federalists, because they supported the Bill of Rights and individual freedoms. The Federalists, like Adams, were the bad guys, passing the Alien and Sedition Acts, ramrodding Federalist judges down the throats of the nation even after Jefferson had been elected but not yet taken the oath of office, and the Federalists like Hamilton opposed the Bill of Rights.
The Federalists wanted a very strong central government, and weak states rights, few civil liberties---sounds a lot like fascism to me.
But then, somewhere in the 1930s and beyond, it seems that things got reversed, and a strong central government is what was advocated by the good guys, doing good things like integration and civil rights--yes using the power of the government to promote civil rights, not to take them away. The strong Federal government was used to give power to the people. One could argue that this started with Lincoln, in some ways, or with Teddy Roosevelt who used Federal power to create parklands for the people....
Now, today, what does Federalism mean? The Supremes just voted to reject the power of the States to regulate med mj. It was the "liberal" judges who supported the right of the strong Federal government to deny the rights of the people to make their own decisions about this.
So, to me, things have gotten really twisted and perverse. The Anti-Federalists, the ones who want power in the hands of the people, seem like O'Connor and even Thomas (against the eminent domain in the Connecticut case), whereas the Federalists are the ones who want the Federal government to be strong, even if that means helping Bush.
This seems really screwed up, but that's the current situation....