Okay, so I just went and checked the exact quote where Sakaoto allegedly said that the Primes were non-canon.
Here it is:
"The games that I've been involved with in the Metroid series have been on the NES, GameBoy, Super NES and the GBA. I actually didn't have a lot of input on the Prime series. But when they're doing with Other M here, it's not so much a different universe, it's just a different part of the story. You can't say that there's no relation here; it's probably best to think of them as being in parallel in this world."
He's not saying that they're not canon, just divorced from the main story.
Which we've known since Prime 1 came out.
Yep.
Looks to me like people are pretty much making stuff up completely to try and villify a poor chap who's probably a perfectly decent guy just because he made one game they don't like, despite the many good ones.
--
Something something something
^Poorly disguised anti-caps sig