So first let's look at the Mewtwo direct.
Magolor also shows up at around 6:15 at the very beginning of the miiverse stage, note how literally every other character there sans the Pokemon are playable or a part of a playable's moveset. At 22:19 you can see the Lor Starcutter, and if you didn't know, is heavily associated with magolor, it's his ship, and if Magolor were to get in, that would be a obvious candidate for his final smash, well it shows up as a trophy, not a big deal right? Well, immediately afterwards, Mega Mewtwo Y and X show up, and one of those (Y) ended being Mewtwo's final smash and Mewtwo was revealed this direct.
Now let's look at something outside of the direct. At first glance it wouldn't seem odd that Magolor has a trophy and the Lor Starcutter has one right? But when we put in some context, it starts becoming pretty strange. For example, did you know that neither a normal Waddle Dee, Bandana Dee, Dark Matter or Zero have a trophy? Think about that for a moment, the most iconic enemy, the fourth main character, and outside of Dedede, the main antagonists of the series don't have a trophy, but Magolor has one? Isn't that kind of odd that those titans can't get a single trophy, but both Magolor
and his ship can get one? It's pretty clear to me Sakurai is, at the very least, giving him a lot more attention than the others who are all more important than him, and I don't know about you, but I think this is kind of fishy.