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I think that they just chose not to use Wally as well. The anime has hasn't really had the best track record when it comes to using the rivals from the games. They skipped Silver, Cheren only appeared as a Gym Leader and Hugh never appeared either, although it would have been difficult to adapt his storyline without incorporating the time skip or using Team Plasma effectively in BW. Wally's role was pretty minimal too, especially in the original R/S. They tried to expand his role a bit in OR/AS, but he only appears a couple of times before you face him in Victory Road. The anime could have expanded on his role and character further, but I don't think that they were interested in doing that. AG wasn't interested in giving Ash a rival outside of the Hoenn League too, so that could have been a factor into their decision as well.