IL2CPP is a fully-supported scripting back end that can be used as an alternative to .NET when building projects for Windows Store. When building a project using IL2CPP, Unity converts IL code from scripts and assemblies to C++ before creating a native binary. Refer to the Unity Manual page on IL2CPP for more information.
IL2CPP is only supported when targeting Windows 10 SDK.
Is something described here not working as you expect it to? It might be a Known Issue. Please check with the Issue Tracker at issuetracker.unity3d.com.