Class handler system
IServiceProvider
So you decided to reinvent the IServiceProvider Interface :-) which

Defines a mechanism for retrieving a service object; that is, an object that provides custom support to other objects.

Your public interface IPandaClass { } is exactly the same. I guess you forgot to mention that it has the GetHandler method or otherwise it would be completely meaningless.
Then we read:

This interface is implemented by a class or value type that provides a service to other objects.

This is the missing GetHandler method.

Generics vs strings

RegisterHandler(&quot;messages&quot;, Utilities.CreateInstanceOf&lt;MessageHandler&gt;());


Instead of hardcoding strings you could use generics and derive the name from the class name or just use the type as a key.

Dependency Injection
Do you really need all classes in one handler? Have you tried something like Autofac etc.?