Nothing wrong with 2%. Yes it has less fat than whole milk but at least as much as soy milk and much more than rice milk. And you can eventually transition to whole milk and give him more fat in other ways - cheese, avocado, meats, flax oil, etc.
Personally, I agree with your Ped and plan to wait until at least one year for all dairy - but I tend to be cautious and DD has had intolerance issues herself.
My friend's Ped had her do the following:
First three days: 1/3 milk with 2/3 formula in all bottles
Second three days: 1/2 milk with 1/2 formula in all bottles
Last three days: 2/3 milk with 1/3 formula in all bottles
Then all milk. Also expect intake to go down once on all milk.
But I don't know how my Ped recommends yet - this is just what my friend did. I'd call your doctor to be sure.