Stericson and DDChains have come up with a solution for apks needing root permissions.
Its called Root Tools
RootTools provides rooted developers a standardized set of tools for use in the development of rooted applications. In the end, we will accomplish this by providing developers with robust, easy-to-use libraries that will drastically improve development times as well as promote code reuse. This project is open to any proven developer that feels they have something to contribute. By pitching in together we can streamline our own processes, improve the effectiveness of our apps, learn new techniques, and provide a better experience for our users.
To sum it up: We all win.
Happy hacking, Stericson
P.S. If you want to help out, send me an email at Stericson.firstname.lastname@example.org and I will add you to the project.
Check it out!