With Brawl, according to sources @thethirdkoopa has (note: don't apply this to Smash 4), the SSE killed production of a ton of characters.
Like, a ton.
And according to them, the
last "cuts" to make the roster a full 38 characters (Sonic was added in 2007, and this was in 2005)
were...
Roy: They found him boring. He was cut sometime in mid-2005 or some time around then.
Mewtwo: They wanted to partially remake him. They had programming issues with this and was kind of glitchy. So, they cut him sometime in late 2005 or early 2006. He was much further in development than Roy though.
So yes, it was the SSE that cut those 2, and a lot of other character (ideas) then.
Don't expect something like that to happen again.
There will be no equivalent situation to that again.