My son started off loving Elmo, and then he became a Pooh freak! As he has gotten older, he isn't into Pooh as much. But he is five years old, and his lovey is still the Pooh bear that we got him when he was three. He sleeps in Pooh PJs (we call them Pooh-jamas) and has Pooh on his sheets and comforter. The Winnie the Pooh movie was the only one he has ever been able to sit through in the theater. He prefers to play with his Thomas trains and Angry Birds, but he always goes back to Pooh for comfort.
That being said, I would do Elmo for your son. The look on his face when he says his favorite character will make it more than worth it. Also, I think that years later, seeing pictures of his first birthday with Elmo is a nice memory of this time when he loved Elmo so much. It's who he is RIGHT NOW, and you will want to remember that.
You have plenty of time to get him into Pooh bear. My son had a Pooh bear party for both his 3rd and 4th birthdays. :)