My worry is that flat design will lead to less information density (because of the decreased emphasis on visual hierarchy and separation through 3D effects) and lead to a downgrade in functionality for some apps. Honestly, I wouldn't be bothered if Tweetbot stayed the same.
Given this pre-existing diversity, the apps that are really going to need to change or look out-of-date are the ones that made the most use of (or styled their custom controls most closely after) Apple's vanilla UIKit controls. I don't foresee apps that take their own approach to UI (such as TweetBot, AmpKit, or Digits) having to change much; in fact, I really hope their designers can see beyond the march of fashion and don't abandon certain types of interaction cues purely because Apple has.
The thing to remember is that "flat versus skeuomorphic" is a false dichotomy – style is a tool, not an end product.
http://www.propellerheads.se/products/figure/
If all flat design apps are like that, things won't be too bad.
Interestingly, their other iOS apps are totally the opposite, and are pinnacles of skeumorphic design:
This layering of design language creates a useful divide between areas of functionality that can't be achieved when you're limited to "flat or skeuomorphic" as a binary choice.
That seems like a very silly worry, given that visually rich design is demonstrably worse for information density, whereas “flat” design is demonstrably better for it.
Your argument of “decreased emphasis on visual hierarchy” has the design principles entirely backwards, especially when you look at apps like Tweetbot vs. iOS 7’s visual aesthetic. Whatever density is reduced in iOS 7 has nothing to do with its flatness, but all to do with the designers’ conscious decision to give UI elements more breathing space. But I can point you to dozens of iOS 7 examples that are more information dense now than in iOS 6, and the main reason for this is the flatter, simpler aesthetic requiring less whitespace to make information identifiable.