But yes, I'll work on that.
That could work, but the only solution I can think of which prevents your setup from needing even more 'plot armor' involves direct PC conflict (which you might or might not want): What prevents your gritty 'iron age' heroes from walking over to your 'four color' area and stopping crime forever? The only thing I can think of is that the 'four color' heroes see the iron age guys as villains, themselves.
Unless you're going to force characters into staying in their intended cities, you will deal with stranger in a strange land incidents any way you slice it. I swear this stuff is candy to a player. They want to stand out in some way. Why not play a gritty anti-hero who refuses to play by the rules in a city where everybody else pulls their punches?
If you keep both cities split off from one another, then why have them both at all? It starts to sound like you've got two games on one server. If you stick to one style, then you can focus all your energy on a single place, not have your playerbase split across two grids, get by with less plot armor, and also allow your players to be more certain of what sort of world they're playing in. It's like I said earlier. You don't have actual source material to rely upon, so you have to be concise and consistent. Your weaker players will strain the cohesion of your setting until it's just kind of a mess. Your stronger players will be unsure of what they should be doing and will need to ask you all the time if this or that is okay.
Regarding M&M stats, one thing which has never changed across 1e, 2e, and 3e is that M&M actually requires an especially critical eye on a PC's proposed stat block. There are a zillion things the game technically allows you to do which is stoopid broken OP or in no way, shape, or form fits in any sort of comic book world. Sometimes the problem is subtle, but is a one-way ticket to WTFsville. I don't just mean hella-broken power/advantage/skill combos, either (of which there are unlimited amounts. I wish I could remember some of the imaginative and completely fucked stuff we saw at Crucible City). With some imagination, you can squeeze an absurd amount of fuckery into a small amount of power points.
If there's any advice I can give you, it's this: Before you open, get really, really, really good with Mutants and Masterminds. I mean seriously, mega-fucking good. Then start trying to make the most powerful characters you can within the confines of whatever rules you're going to apply to your playerbase. I mean it. Break that shit and break it good. Then revise your rules and do it again. Eventually you'll reach a state where your rules will generally guide a player into making a fair character, and you'll be skilled enough to spot problems on a statblock even when they follow all of your rules. M&M is not one of those systems where chargen spits out characters who are even roughly matched in power and utility. It's easy to make a broken character, and I've seen plenty of M&M games fail because they approved any legal statblock.