Right now my theory is that his dad will end up either in jail or dead, and he'll take over as the big bad from then on.
That's my hunch as well. He'll probably be one of those "gray area" villains (maybe even an anti-hero). One of those characters who aren't entirely bad (and occasionally do good), but are still hero's adversaries.
What interests me is how he'll get his training. Will his father train him? Will he leave Starling city as Tommy, and return as Merlyn? Laurel addressing him as just "Merlyn" seemed a bit like foreshadowing. Maybe.