I don't think there'll be references (assist trophies, items, stages and the like) to 3rd party franchises unless they are represented by a character.
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I'd like to see Alex Roivas, from Eternal Darkness. Or even better yet, Karim. I'm not sure if Nintendo owns those characters or if Silicon Knights does. Little Mac would make a nice Assist Trophy.
Ooooh. Hmmmm. That's a very, very interesting one. I would, like DaaMan, love any sort of reference to Eternal Darkness, it being in my Top 5 GameCube games and tied with Pikmin as best new IP last generation. And since it's a new franchise that arrived after SSBM, it would definitely add variety to Brawl.
Still, the dark nature of the game clashes horribly with Smash's atmosphere - Roivas would be even more out of place than Snake. Plus I think Nintendo wants to forget not only the game, but that whole Cube era. So I'm not holding my breath for an ED character. If we're lucky, we'll get an item triggering a sanity effect. That would be awesome.