I really thought, and still think it's sad that they put Pichu and Jigglypuff in SSBM. They were pathetic, as Pichu was weaker and it hurt itself. Whilst Jigglypuff was better, it kinda focused as a defensive one, and defense isn't always the best strategy in this game. I loved the arrival of Mewtwo, and along with Pikachu is my favourite character,
If they did put another Pokemon in SSB3, then I think it would be a legendary, and it would be either Rayquaza or Groudon. Why them? Because Rayquaza would be able to actually float and attack, whist Groudon would be a a Ganondorf in Pokemon form. They wouldn't put Kyogre in, since there's no water in many of the stages.
A character I'd love to see in (but will never happen) is Chain Chomp ^_^ It's indestrutable, and that's why I love it, but many people will loath it because of it's cheapness.