So far, I like the idea of an academy of some sort as the core of where the characters come from. Regardless of what other decisions are made about the setting, scope, and genre, I'd like to keep that core concept intact.
The academy serves as a training ground, of course, and training for what is the next core question. As I see it, the two options are:
1. Training to do battle with supernatural / alien / futuristic creatures and bad guys. This would have more of a "gritty" feel to it.
2. Training to do battle with other supers. This would have more of a "4-color" feel to it.
These aren't necessarily exclusive options, but the idea of going 4-color vs. more of a gritty theme does sorta make the decision for us. You could have 4-color ghosts, demons, and vampires and you could have gritty supers, but I think I'd like to keep the genres from intermixing for now.
In terms of setting, the modern world makes the most sense, and it seems that everyone is in agreement on that. Different takes on the modern world are possible, of course, including somewhat retro and somewhat future takes on it (for example, I like the idea of a post-2012 as being a false "apocalypse", but having some effect on humanity creating supers).
There's also the question of what sort of stories we want to explore. The "academy purpose" question above can address this to a certain extent, but within either option are genres such as horror, espionage, crime-fighting, conspiracy, weird science, and so forth.
For now, let's vote on one of the following options:
1. The Academy trains young supers to do battle with rogue supers causing trouble in the world. This would be the "4-color" option.
2. The Academy trains young people with extraordinary abilities to defend Earth against the encroachment of aliens/supernatural horrors/etc. This would be the "gritty" option.
Once we have this decision made, some of the other decisions become easier to determine.