As much as I dislike 2003 in comparison to Brotherhood, i think they did give more justification and had a bit more buildup for Alphonse’s whole identity crisis. In Brotherhood they cut the whole bit where Al can’t remember any of the people he used to know and tells Ed he thinks there’s something wrong with him, thus prompting Ed to bring up the ‘thing he’s been meaning to say’ instead of it just basically coming out of nowhere.

Ed not telling him one thing doesn’t seem like that much of a cause to start on that 'doubting your entire existence’ road is all I’m saying.