Hopefully F.lux works still. That was the worst thing about using a new, unjailbroken iPhone and iPad. Especially now that iOS 7 has a lot of white UI.
Removing F.lux didn't do anything so I thought it was Mobile Substrate, but removing that didn't do anything until I rebooted the device so I can't be sure.
Other apps depending on Mobile Substrate work OK so far, so don't let it turn you off trying things out.