The Pokemon secret, i didn't realize there was one, Fatelbrain found it, and it was hidden pretty deep.
But the secrets are
Bottom Path Area 1
After you hit the switch with the yellow save point, You have to make it back WITHOUT dying and WITHOUT saving on the way, There should be a glowing ball, and you gotta make it down there without dying and collecting it. then you may save.
Bottom Path Area 2
So After you defeat MissingNO Endurance Pokemon Battle Thing, You need to follow this path. https://prntscr.com/1pg1rv
Upper Path Area 1
After the second moving box thing, (The save before the cherry spinner) You will see a spike be triggered and go left, you want to go where that spike used to be, once you get down there, you will have a fast moving box which you have to move along it like you did with the other boxes, enough said. Although if you died on MEDIUM, and MEDIUM only and saved at the wuss point and died there at least once, try not to fall back to that save.
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Upper Path Area 2
I Really have nothing to say about this one, it shows itself, it's way to obvious :p
I hope this little guide helps. :D