So you want Black Doom, a generic alien from a spin-off of a sonic series, to take the place of the oldest and greatest villain in Sonic History? Well, even ignoring the obvious statement that I'm fairly sure everyone else is going to make, I'll talk in the language of unbiased (as much as I can be) chances.
So, Eggman/Robotnik. He's literally as old as Sonic, and older and more important to the franchise than every other character in the game. Shadow is just a kid compared to this guy, let alone Black Doom, who appeared in one minor game. Eggman has a long list of things he's done, some of which are quite evil. Black Doom has tricked Shadow a couple of times, nearly destroying the world. Like Eggman did in the previous game... and in CD, when he took it over and everything was miserable... and even then, Black Doom did nothing directly, instead choosing to have Shadow do all the work, who then enlists the help of who, originally? Eggman & Rouge. Eggman. Remember him? The ******* who traps animals in machines so that they can use their life force to power it? Yeah. But anyways, Eggman has accomplished more than Black Doom can, because Black Doom isn't coming back for another game.
The next point, is that Sonic in Brawl is there for a couple reasons, the biggest ones I can think of being advertisement/selling and because fans that were foaming at the mouth demanded it. Throwing Black Doom into Brawl would be like trying to advertise a bad game, and that's a really bad idea for a game which tries to get you into other good franchises. Because if they play Shadow the Hedgehog first, and get sick of it's poor controls and story, they probably won't try any other games they don't recognize from Brawl. That seems a bit extreme, but it can also extend to those casuals who never played the game, but heard about it somewhat. The other thing is...
Well, those fans that foam at the mouth? They aren't foaming for Black Doom. Some of them might be foaming for Shadow, I don't know, but if they made a list of characters that they wanted, Black Doom would be very low. On my list I doubt he makes the top 20, and although the Sonic franchise has a lot of characters, 20 is still a lot for any franchise, except maybe Final Fantasy, and I mean the entire franchise, which has a different cast for every good game, and some of the poorer ones. I've never seen the idea of Black Doom advocated anywhere else before, and from what I'm seeing in this thread, there aren't many supporters at all, and many more against.
And yeah, some of Eggman's recent plots haven't been the greatest. Really though, he's always had his fair share of bad plots though. Finally, one thing that bugs me, though I might get flamed for saying it.
Ganondorf =/= Black Doom.
Ganon/Ganondorf == Robotnik/Eggman
Black Doom == General Onox (Oracle of Seasons)
And in conclusion, I highly doubt another Sonic character will be playable, but if they do, it won't be Black Doom. It probably won't be Eggman, sadly enough. It'll probably be Knuckles or Tails, although I really see Tails as Assist Trophy material. Too bad, he could have a cool moveset. It might be Shadow, although I am loathe to admit it. Shadow stopped being a cool character once they brought him back to life, in my opinion. But that's another subject entirely.