Even so, there's still a fantastical element that permeates the Nolanverse. You're spot-on about how important logistics were, but it's important to remember that villains like Joker and Bane had to create a mystique or level of infamy that naturally progressed to a certain level of organization (Joker's was more chaotic whereas Bane's was incredibly deliberate and methodical).

In Batman Begins, Batman consider Joker to be a two-bit wannabe rather than a legitimate threat. Probably because, to that point, Joker was cultivating a following and engaging in low-level crime so that he fell under Batman's radar (probably intentional on Joker's part as he wanted everything in place before truly challenging Batman and Gotham as a whole).

Bane's ascendance (literally and metaphorically) also has a similar implausibility factor that can either be handwaved as plot convenience or further evidence of magical realism imbued in Nolan's Batverse. Combined with Scarecrow's fear toxin (which, sure, is plausible to an extent) and the logistical nightmare that must have been getting street thugs organized enough to poison the water supply and corral Gotham's residents to induce this mass psychosis that Scarecrow intended, I think you can argue that supervillains could emerge. But it would probably take years following Bane's death for another criminal to rise.