Has managing all your game objects in non-Monobehaviour classes worked for you?

I figured out how I could manage a gameobject as actually a component(variable) of a non Monobehaviour class. I realize this may create great overhead perhaps in the future but it has been working really great because I get a lot of control and direction I wanted.

Anyone else who is doing this meet any difficulties down the road which I may not be seeing with this design scheme?

No significant overhead of this approach. Plenty of bigger games will do everything in their own C# code and only use Unity to render and receive call backs.

Oh, thats good to hear. I was worried I may hit some kind of wall later on.