I don't think anyone here is against MX being the villain because it's "obvious" and if they are, it's a poor excuse.
Actually, I wouldn't mind if there was a twist in the plot and MX wasn't the main villain, because I like a suspenseful storyline that keeps me guessing.
That being said, I have no doubt from watching the Secret Ending that MX is an evil villain. But this wouldn't be the first time that we've seen this type of plot twist. We played through KH1 thinking Maleficent was the head baddie, only to find out that it was really Ansem, who really turned out to be Ansem's apprentice, Xehanort.
I say there's a possibility that DS could have turned on MX and started controlling him, but the fact that it's been done before makes me hope that this won't be the case. If this turns out to be true, I hope it's more complicated than MX simply losing control.
Plus, while the actual events of the Secret Ending don't reveal whether DS is controlling MX or not, the
way the events are shown doesn't make it look that way. VAT seems to be focusing all their energies on destroying MX, and DS looks like a mere interference in accomplishing their goal. Terra goes straight for MX, and DS hardly does anything outside of fighting Ven and Aqua.
So while I wouldn't rule out this theory just yet, it's not very likely from what the clips show us of MX and DS.