Melee had 11 Secret Stages, Brawl had 12 Secret Stages, so I'm gonna round it up to 15 possible Secret Wii U Stages...
I assume the one in the Direct was the Starting Stage List, whereas Congo Jungle and Smashville, seen in the site update, are secret stages...
1. Congo Jungle (64)
2. Dream Land (64)
3. Yoshi's Island (64)
First off, I think we'll see the three stages that were ported from 64 to Melee all return, so these three. We don't have a "normal" Kirby or Yoshi level yet, so they'd be nice. Yoshi having three stages feels a bit off, but then again, Melee Yoshi Island is just from Super Mario World.
4. Pokemon Stadium 2
Spear Pillar won't happen since Palkia is a PokeBall, and I can't see them not giving Pokemon a retro stage.
5. WarioWare
6. Distant Planet
7. Flatzone 2
I think these three will return from the 3DS to give Wario, Pikmin, and GW a retro stage, that way all the non-3RD party series have at least one retro stage in the Wii U Version. I actually don't think GW will have a new stage this time around. I think Wrecking Crew will be his home-stage.
8. Mario Bros
They brought back 75M, I can see them bringing this back.
9. Smashville
10. Magicant
11. Mute City
Both these stages seem like they could be ported to the Wii U easily enough, and I don't see Sakurai taking the time to make more original Mother/F-Zero Stages.
11. New Pokemon Stage. It's one of their biggest series, I think we'll see another new one. Hopefully a city locale to match the 3DS layout of Elite Four/City. I'm thinking something from Black and White.
12. Wind Waker HD Stage. There's a lot of Wind Waker Trophies we saw, I don't see it being ignored, stage-wise.
13. 3rd Kid Icarus Stage. Probably something Underworldy, like a scrolling stage based on the original Kid Icarus. Sakurai bias, ahoy!
14. Bowser Stage. Something for Bowser and the Koopalings to call home. Bowser's Castle? The airships? Or Bowser World from 3D World even?
15. DHD Stage. Probably based off one of the Lightgun games, or a combination of them. Bet we'll see it in the reveal trailer.