Chainfire reveals that certain changes in the security policies of AOSP's kernel, SELinux, make the latter even more secure than before. Referring to it as “SELinux on steroids”, Chainfire states that the kernel now prevents root apps to run in the /data partition, thus breaking them “in new and exciting ways”. This means that making your root app work will be a tad harder.
Additionally, it appears that the latest version of AOSP runs on the experimental ART runtime by default - up until now, Dalvik was the preferred runtime. ART is considered to be superior to Dalvik, as it provides better performance and increased battery life, but most apps have certain compatibility issues with it. What's more, Chainfire says that the combination between the new runtime and the latest version of the SELinux kernel might cause even greater system instability when a root app is making an unauthorized or incorrect query, resulting into constant reboots.
It is highly probable that these changes will make it to a future version of Android, be it 4.4.3 or even 4.5. Luckily, Chainfire built a new version of its root management tool, SuperSU, which successfully bypasses these newly-added changes in the most recent AOSP builds - great news for all Android root app developers out there.
source: +Chainfire via XDA