I don't normaly read interest checks with more than 30 replies, but when I do, I'm interested. 

After spending a small eternity reading I want to contribute, so here are my opinions on what have transpired so far... 

Three threads portraying three different locations: 
I like it, it would get mighty crowded if we tried to cram ca twenty superheroes into one location. Crime wold go way down over night.

Liquid vs Solid time:
While liquid time has its advantages in a game like this, very few players can handle three different timelines that take place at the same time. I'm not trying to be condescending, but experience tells me that this a typical thing that can become “too much”. Solid time, while not the best of systems to use in a superhero setting, is easy to grasp and follow. Every character is in one location at any given time (unless their freaky super powers say otherwise). It will also force players to interact and give exposition once a character travels to a new location. They won't instantly know what is going on, and so one of the players in that location has to tell him/her. Good roleplaying bonuses all around. My vote is for solid time.

The three cities explained:
I like the idea and diversity of the cities. I think you've covered the three big “comic book cities” so everyone should have a place where their character would feel the most “at home”. 
Also, it's easy to find real-world cities that could mirror the cities in the game. Like this:
Grimmarch – London.
Claychester – New York.
New Skywell – Tokyo.


Last but not least, questions. 
Being a superhero-rp, there is always the question of limitations. Has the GM(s) given this some thought?
I'm not thinking so much about power levels, but more on origins. In some worlds things like magic can clash with the setting, of perhaps aliens shouldn't exist. Perhaps the eternal war between heaven and hell is a bit too much of a side note... Just throwing the thought out there.