Will iOS ever allow developers to create native functionalities that can go beyond apps, more like plug-ins?

No. This is unlikely.  Because the inevitable conclusion of such a move is unreliability. Applications rely on existing in precisely controlled environments. The smallest and most benign changes to those environments can break the app in subtle and unpredictable ways.  The practice of having third-party software change system-level functionality is popular on desktop computers. But it can be argued that this freedom has led to the experience of unreliable and slowly deteriorating user experience. Apple sees the iOS platform as an appliance model. When the user runs an app they can rely on the fact that it is going to perform as the developer intended. They can do this because the developer can rely that on the software running in an environment the manufacturer intended. There's no doubt that this thinking places restrictions on the device. But in Apple's calculation, reliability and simplicity are more valuable.

No. I can safely say this will not be allowed, and not just in iOS 7. What the question seems to be talking about is more of an Android thing, and with the kind of control Apple keeps over its products -- especially iOS devices -- customization on that level will not happen. That's a good thing, too, since the security of the platform would drop dramatically with that addition like security on Android has. EXAMPLE: Lets say a developer releases a plug-in for iOS that allows a user to toggle Airplane mode using the Ringer Switch on the side of their phone. (That's a weird example, but go with it) But, unknown to the user, the plug-in also transmits important information to the developer's servers regarding security on your phone, such as the device's UDID or sent usernames and passwords... even your Credit Card information. The user would have a terrible time trying to figure out the problem, and if many plug-ins are installed it would be very difficult to find out which one is causing the problem. Could Apple control this? Theoretically, yes. But there are apps that Apple shuts down that were previously approved but found to violate rules, and if Apple has trouble keeping on top of all those they would have even more trouble with plug-ins. A major advantage of the App Store is knowing you're safe when downloading any app -- even if it looks extremely suspicious -- since it is tested and proven safe. Plug-ins would be much more complicated to secure in this manner. Not even Siri has access to WiFi settings, for example, which shows how much Apple takes device control and security very seriously.

Customization is not always a wonderful thing. Lets say, you add Pinterest as a system wide available tool for making a wishlist. It creates confusion in the mind of users, as in Pinterest popping up as an action in unexpected places (like a diary app or a game app). There are a few ways to do this, and AFAIK, App developers would want some kind of inter app communication protocol too. Apple is obviously aware of this. There are now power users of iOS who would want to do things faster and iOS7/8 would have some kind of functionality that would cater to your requirements. But not in the way you would want. Hopefully.