While Microscope looks interesting (based on an RPG Geek review), I'm not familiar with it and I'm not eager to buy new books and learn new rules just so that I can run/play in a completely different game.
- Get Microscope.
- Get your group together.
- Play several sessions of Microscope to establish a comics history.
- Have one of the players become the GM.
- Let the GM break the history down and make a “reboot” of that setting.
- Set up the PCs as “rebooted” versions of each player’s favorite hero from the history.
- Play as a standard Supers game in your system of choice.
Here's my take on it, using DC and Fate as an inspiration instead of Microscope. Much like DC, these eras are completely unrelated in universe, although people can feel free to use early versions of characters as historical or alt-universe versions if it makes sense.
Golden Age: Superheroes are wild and strange, and generally in their own comic line, unrelated to anything else. This corresponds to a brainstorming phase. Everyone comes up with heroes and villains. Short descriptions, nearly anything goes. This is to create a shared pool of ideas to draw from for the next phase. Also to establish the tone and kind of game everyone wants to play.
Silver Age: Heroes start coming together, their powers locked down to a specific set (Superman doesn't use Super Hypnosis or Super Weaving anymore.) This is a series of VERY short games, a scene or two each. Use the Fate Accelerated rules with On the Fly character creation. Someone comes up with a villain's plot and the group picks a series of heroes and/or villains to add to it. The point here is mostly to tie down these characters' aspects and skills and to get a feel for who works together and who doesn't. Tell stories and develop quips. Don't feel limited to using your own characters. Even here, nothing is set in stone.
Modern Age: A large, sprawling shared mythos where all the characters need to actually make sense together. This is the real game. The GM chooses what bits they like, what the 'reality' of the world is: where do powers come from, what is the setting, is this a supers team or Aberrant or what? Each person picks their favorite character from the Silver age and "retcons" their new history. I'd suggest something like Fate's shared character creation just so everyone knows exactly what's been changed and how the new iterations of the characters fit together.