What makes something canon in the first place? The will of the original author? Fans seem to disregard 'non-canon' material even if it is endorsed by their original author.
It is a strange thing.
Canon is indeed determined by authorial fiat (generally, anyway). A fiction's canon comprises of all works or properties that the creator (or those who hold the fiction's copyrights) deems to be part of a definitive continuity, or whole. This continuity can be defined as a shared timeline, a shared setting, a shared universe, etc. in which the work exists, or works coexist. Spin-offs are not canon, as they by definition diverge from the mainline continuity -- unless the creator(s) state(s) that these spin-offs do exist within the mainline continuity.
Since the creators are the ones who create the fiction, they can define (or market) a work however they choose, since they're the ones who know where the work(s) fit in their continuity. They determine how works relate to one another, and how fans are to treat these materials -- and if a given fraction of the audience doesn't approve, then tough, because Word of God trumps all.
For instance, George Lucas has the main canon of Star Wars (i.e. the film franchise), and he has the Expanded Universe -- books, games, and other Star Wars properties which, while Lucas doesn't work on them personally, are sanctioned by him (and are canon, as they exist in the same continuity as the film franchise). Star Wars fanfiction, on the other hand, would be non-canon, as these works aren't the direct creation of, nor are sanctioned by, Lucas himself. And as much as some segments of the fanbase dislike the Prequel Trilogy, and consider them "non-canon", they are canon by official authorial decree.
Because Smash is a crossover game, its contents are drawn from multiple canons (from the respective games and series of origin). Smash itself has no "canon" in itself, since it has no established shared continuity, especially between titles***.
As has been the case in the past three games, Smash takes inspiration from the canons of the games it references. It respects elements of external canons inasmuch as these elements don't conflict with Smash as a fighting-genre game. So while Olimar in Pikmin canon is an inch tall, he can't retain that size in a Smash environment. So, they upsize him considerably. Likewise, Captain Falcon originated in racing series, and so it isn't canon to F-Zero that he has fire-based attacks; they added those attacks to make Falcon viable as a Smash fighter.
So far as Ridley is concerned, if they want him in, then they'll lift from, and respect Metroid canon as much as they can without interfering with Smash as a game. So if Ridley's size, while canon in Metroid, is an impediment to his playable inclusion, then they'll disregard Metroid canon for the sake of his inclusion. A playable Ridley would be smaller than Metroid Ridley (on average), and so Smash Ridley would not be a "canon" Metroid Ridley. But then again, the Smash series is not canon to any of its constituent game series to begin with.
***The original conceit of Smash was that these fighters were all trophies brought to life. This is a recurring motif in all three previous titles. And the Subspace Emissary campaign had its own storyline and universe, so it can have its own "canon" (i.e. the canon of the SSE). So Smash does nominally have a canon, but its very (very) loosely defined (and hardly touched upon outside of story modes), so it's only important at a surface level. 
's size is not.
