I prefer the current version. You have a bit of tantalizing info about the possibility of aliens right at the start, then he's got some odd abilities which show something odd. When the dog turns up you really start to wonder about alien involvement. I feel a lot of the tension is lost with the clear alien knowledge up front.
I prefer the current version. First, the original version really didn't use any skills or memories from the "old soul", so the setup was largely a waste.
The story makes it clear that the main protagonist wants more than anything to be normal, and is keenly aware when he does something weird. A Pinocchio motif, if you will.
In addition, many of his skills develop gradually, as a result of a failure in the "suppression mechanism", so they weren't as natural as using one's arms.
Overall, I am disappointed that the MC gave up on the special skills, although it fits with the story arc. On the other hand, there is a subtle and ambiguous hint that the skills may not be quite gone.