I agree, I've always thought Wally deserved more. He had such a cool adventure with Norman and Rayquaza and Treecko. He was a dex holder for a while, even though it was just a stand in. I couldn't stand Emerald, not just because of his ridiculous looks but because he wasn't an interesting person you wanted to relate to either, while Wally certainly was from the moment he met Ruby.
I don't remember why they did't pick wally but there was a reason I read about. I think they could have made Wally and Crys know each other in some way and get a bit of story to them in some way just like they did for Dmerald and Crys now.