Suggestions noted. Thanks.
As for hideouts... The Goldwyn Apartments can be used to rest. Or, if you feel like pinching pennies (or dollars), you can rest at the Homeless Camp. I have made a note about the other suggestions at the HQs.
And please don't take what I said the wrong way. I'm not complaining or saying the game's bad (it's not), but it'd be good to have a little extra realism.
Oh, and here's an idea I got from an episode of Batman: The Brave and the Bold. In "Game Over for Owlman!," Batman has to zip around Gotham to avoid being captured by Aquaman, Captain Atom, Plastic Man, Green Arrow, Red Tornado, and Blue Scarab (basically the guys he's been teaming up with this season). He slips into tunnels hidden in various parts of the city (disguised as a hot-dog stand and a bus station booth, among other things), mentioning that he had them installed to get around the city without being noticed (and to get to his hideout more easily).
So what about a series of underground tunnels that have been constructed to help the heroes of Macropolis City? They could be used to get to several "hot spots" around the city, and could only be found if the hero's Brains level is at a minimum of, say, 7 or 8 (to realize that the marshmallow stand is really an entry point, for example). The tunnels could be modified through a Mechanics skill (to keep out villains or curious kids from discovering them) to have camouflage and other gadgets.
I'm full of ideas, so just let me know if I should keep spitting 'em out