I think that they arent that bad (Mali that is), but a civ should be in if it was very influential. I think that Mali at any rate is a better choice than the mongols, who would be great as one of the civs in the first expansion pack of civ4 but not really needed in the original civ4.
I confess that i dont know anything about Mali apart from the gold trade, but it sounds like they didnt manage to promote sciences or technogoly despite of their riches. Also another argument against them is that they arent that ancient (ok i know that usa is in, but that is due to their later develpopment, not to mention that it would hurt sales if it was out). Really can you think of a reason to have Mali in and not Korea?
Also Austria was very important for a couple of centuries, but didnt even make it in one civ3 pack. Ok, the fact that Germany is in would make Austria too much to be in the original pack, but not having it as a civ in civ3conquests for example wasnt utterly fair either

But the pro is that Mali is a civ we hadnt seen before in Civ, and not an insignificant one. I am more against the mongols, and think that they should be replaced with Babylonians, but perhaps then we would have too few warlike civs in the original pack, and since the Babylonians will be in a latter pack i dont really view that decision as trully catastrophic either.
ps: there is no way that Mali was the second largest empire in history, you are wrong there

It wasnt even the second largest land empire. At any rate it was smaller than:
-the brittish empire
-russia
-tamerlane's empire
-alexander the great's empire
-the roman empire.
Even the byzantine empire was larger, and definately so when it still had egypt and the levant. Perhaps you read that it had been the second largest empire in africa, that is probable
Up to where did Mali reach anyway? I looked for maps at google and what i saw was that the empire of Mali didnt contain a vastly larger area than what Mali is today, and that is smaller than brazil, the usa, china, russia, australia, canada etc etc etc. So as far as territory goes it wasnt big, and if you take out the desert it was a rather small country.