Gentlemen?

[K2J]

Dr. Robotnik not being the engineer seems just wrong, if yet it would be hard to assign a different role to Tails.

You could shift it so:

Eggman = Engineer
Tails = Medic
Amy = Announcer

But I personally like the idea of Eggman shouting, "YOU FOOLS! Our Star Post has been contested!" or somesuch. Makes it so the team is comprised entirely of anthropomorphic animals; adding Eggman to the playable list would break that a bit.

Now, who would be the Scout's mother...

[Shadow Hog]

Sorry, but as nice as Bark is, Eggman just IS the Heavy. I can't envision it otherwise.

Also Blaze would make a better Pyro.

[K2J]

But then it wouldn't be Sonic the Fighters 2, it would just be TF2 with Sonic characters...

I think I've got the team name acronyms down:
Creating Habitats for Anthropomorphs and Others, Syndicated (C.H.A.O.S.)
Corrupt and Narcissistic Takeover of Regions and Lands (C.N.T.R.L.)

[Shadow Hog]

Why would we want it to be StF2, anyw... wait, StF2, I just got it.

Meh, I still prefer the "TF2 with Sonic characters approach.