there should be more cases and accessories for the 5 so i would say that the 5 has a better resale value. also it is suitable for everyone in terms of looks, compared to the 5c that looks less premium looking
iFunbox is free, iExplorer is paid. unless you're on iOS 8.2 or lower, access is considerably restricted right now. iOS 8.3 patched some security holes that kinda broke the app management function. you can see the page before this for the kind of message that you'll get when you try to access apps via these file manager softwares. you can still browse and extract other basic stuff though like contacts, music (i think), etc

but if you're talking about a file manager app on the phone, i don't think there is any that would allow access into system files unless you have a jailbroken device