Most of the inconsistencies can be dated back to smash 64/melee not being as faithful as sakurai had yet to hone his meticulousness. Compare Any veteran from smash 64 and how faithful they are (Link's taunt!?) to, say, MEGA MAN, who is literally the most faithful character recreation we've had to date. Sakurai has gotten much better over time. Not to mention the fact that smash 64 evolved from a non-nintendo-all-star-fighter into what it is now.
They likely reused a lot of moves and abilities from the early alpha of the game and shoehorned those abilities onto nintendo characters. Same with the stages.
As for rayquaza, you can just blame that on subspace being not at all consistent with the nintendo universe. I mean, ganondorf looks at computer monitors!
Subspace is whatever! It makes no sense. Maybe rayquaza was looking for fish to eat!? Who knows.
All I know is that since KI:U, sakurai has proven to want to be as faithful to the character and fan expectations as possible, and it really shows. It'll be interesting to see what he does to the remaining characters we haven't seen.