While I can't speak from the DFRPG side, since I'm hardly a master of the system, from a pure story perspective I always found a lot of the Undersiders to be pretty crazy strong right from the start. Grue and Regent took a while to get really scary, and Imp doesn't enter the picture for a while, but Skitter, Tattle, and Bitch struck me as forces to be reckoned with from the get-go. Skitter hospitalizes one of the strongest capes in Brockton Bay all on her own right at the start of the story, and the Undersiders beat the numerically superior Wards, plus Glory Girl and Panacea, in a straight fight very early on, and with Skitter and Bitch both holding back from any potentially lethal use of their potent powers.

I took a look at the thread Sanctaphrax is talking about, and that depiction seems to be a great way to represent a pure mortal in a cape world without needing extremely high skill amounts!

As Sanctaphrax said, it's not really about racism, it's about the conventions of the Worm world. You pretty much need a Thinker or, failing that, a ton of really serious superpowered muscle to be seen as one of the city's strongest forces.  Even the most competent normal can't hold a candle to Skitter's unbelievable multitasking, Coil's risk management, or Tattletale's information-gathering and psychological warfare.

A standard comic book "normal" like Batman would be a Tinker in the Wormverse anyways given his ability to produce and/or manufacture a variety of bizarre and specific tools and weapons on demand, which leaves a true Wormverse normal with nothing but their wits and their guns. Wits will not suffice against a Thinker, and guns will not suffice against quite a few different kinds of capes.

If you're really determined, you can run with it, but you'll need to come up with a very compelling reason as to why this gang is taken seriously when they're headed up by, and taking orders from, a non-powered individual. In the eyes of the nastier types in Brockton Bay, not having powers makes you weak, and if you're a powered person taking orders from a normal, than to them you're weak too. Flayer's gonna need one hell of a rep. You might consider having him pass himself off as some kind of Thinker for appearances when in fact he's just a near-genius level intellect without the benefit of any special powers. This accomplishes your goal of retaining his normalcy while also granting a plausible reason for him to be taken seriously within the community, as well as a potential weakness and plot hook for PCs to explore and exploit. His parentage will also make establishing such a facade fairly easy for him. Keep him well away from Tattle, though!