I really doubt Harry is literally a younger version of THE Merlin. I don't want him to be that, either. It's too simplistic, it's almost the classic time travel time loop story.
But I do think that there is some strong connection of some sort between Merlin and Harry, and I suspect that Harry might, way down the road, master magic at Merlinian levels. But that would probably be off-stage and post-story. I suspect Harry will eventually meet Merlin, too, either because he's still out there somewhere or through time travel.
(Another possibility that I've toyed with, though I don't think it likely, is that the culmination of the series will end with The Magic Goes Away, i.e. the world becomes non-magical and the supernatural powers fade away. But I don't expect that.)
