In an ideal world where Ewan was given a workable script and a director who could direct actors it would make sense to have Obi-Wan the PT protagonist but there isn't really enough Obi-Wan to put him the center of any one film bar the last.

Unless...

Rather than having a trilogy protagonist it would make more sense to have one per episode.

Padme makes more sense in TPM (she has a mission statement to fulfill).

Weird as it sounds Anakin has the nearest thing to a story role in AOTC.

ROTS is practically Palpatine's but in terms of a hero it's the nearest you get to an Obi-Wan that connects to the OT (he is more relaxed, he has moments where he shows genuine concern for his former charge he looks and feels more like Ben (when he isn't doing cart-wheels or juggling light sticks).