Being a clone most likely was a factor in Pichu's departure, but the catalyst was that he got axed for the next Gen available during Brawl's release. Pichu was Gen 2, which Melee was happily advertising. Unless my dates are screwed up and it was part of the Ruby/Sapphire age. Mewtwo was also popular, and again, axed for more up-to-date pokemon. And let's not forget Lucario's "similarities" to Mewtwo. I mistook him as a related to the Mew family back when he was new as a Brawler.
Lucario will not be returning as a fighter. It's as logical as DLC being evil.