Here's the way I play matches, stage-wise:
Opening stage-ban: Yoshi's Story. Ness just doesn't have anything there, except an easy recovery from the walls, and the blastzones on the sides are just too close for him. Unless it's against a Puff player, in which case Mute City hands down.
After losing the first round, counterpick: Against Marth or Roy, Corneria (they're just too dangerous on Green Greens with the side blastzones so close.) Against anybody else, Green Greens, probably, unless I think I can nail a Fox or Falco on Pokemon Stadium with the LBK infinite.
What stages do I hope to get with the first random selection? FD is solid. I don't like battlefield too much. DL64 is okay, I like the far blastzones. FD is my favorite of the neutrals, probably.