I can not see Tommy being an effective villain. The type of training he would need to face Oliver would take a very long time. Plus he would know it. He has seen what Oliver can do. He would know he would not be able to stop him. Plus all he would need to do is tell Dectitive Lance Ollie's secret and puts him in jail right away. Tommy taking over for way too obvious and would be totally unbelievable.
I do not know what they will do. Maybe Tommy should be killed off. That would be more interesting. The effect on Laurel and Oliver. It would become a full out war between Oliver and Malcom.