This is stupid speculation on my end, but maybe his Mega Evolution could be a part of his character customization. To my knowledge, Sakurai has not revealed anything about what the customization is about, and, since he isn't interested in competitive play, the customization could lend itself to interesting situations, and there could even be custom settings for each character. In the case of Lucario, his customization would be his held item, like from the Pokemon games. Among other things, one of the items could be Lucarionite to change his FS into MEvolving, for example. A system like this could help fix Mewtwo's Final Smash problem, but again, I'm just speculating for the sake of it. Make of it what you will.