Actually, there is. Argonians and Dunmer have hated each other since the dawn of time, as have Dunmer and Nords. As this game is in the Second Era, before the Empire united them, and before the Red Year and all those other things that made them put aside their differences, there is no way in hell that they would form an alliance.
And the only time Redguards and Bretons get along is when they kill Orcs (who only became citizens in the Third Era, some 400-odd years after TES Online).
And the supervillain teamup is just stupid.
Past hatred does not make future allianeces impossible in any way.
The Dunmer and Nords have teamed up at least once before to take down Dagoth Ur, and the Argonians never really gave a [censored] about thier enslavement, even after the red year all they did was take back the old part of Black Marsh and sit there when they could have commited mass genocide on the Dunmer.
This "hatred" that would make it impossible is unfounded.
Also, Nords, Redugards, and Orcs are known to respect eachother greatly becuase of thier combat prowers. Furthermore the Orcs were part of the second Empire. It is not beyond reason that former enemies who have great respect for eachother could team up.
As for the badguys, its more like Tharn's family and Manimmarco have teamed up, becuase Mannimarco promised them power, but Manimmarco is selling everyone out to Molag Bal. The three forces are not all allied with eachother, or working for the same goals.
It is even stated directly in the scans that The Impeirals dont know Mannimarco is working with Molag.