No, Ganondorf was just an addition. Zant was still there, still a villain and had not changed the established role he had since Dungeon 3. Since Dungeon 3 he, admitted to following a "God" and was an obvious follower--actually, if the Skull Kid had just been tempted by the Mask itself, I wouldn't be so upset, at least his integrity as a villain would remain. But no. Instead they changed it so he was never a villain at all, effectively replacing him rather than just adding Majora's Mask as the Bigger Bad.
From the beginning it was established that the POWER of the mask corrupted Skull Kid. Not the mask itself. In fact, Tael even says this right before the mask reveals it was actually the mask itself.
Again, no, there was no hint whatsoever that the mask was alive and the game characters always stated it was the power that corrupted the skull kid. And this was cool. It made him a tragic villain and a pretty good one, unlike Ganondorf from tWW, which just went against his previous character. If the skull kid had at least remained a genuine villain, I wouldn't be upset. But he was replaced. Not just replaced by another villain, but by a villain with so much less potential.
Before the reveal, we had a villain hell bent on destroying Termina. Why? Because he was filled with hatred over the loss of his friends.
After the reveal, we had a villian hell bent on destroying Termina. Why? ....Just cause.