CLR apps require just in time compiling which can take a little time to first run. So this should speed up opening the apps.
The biggest difference with NGen is the fact that .NET Native doesn't ever "fall back" to JIT compiled code. There are other differences--refactored runtime, static-optimized libraries, static marshalling, etc.--which can be seen by the perf wins over NGen. We're seeing 40% startup performance gain over NGen apps for top Windows Store apps.