The Thalmor don't want to do what the Dwemer did. They want to do worse - they want to take the entire world back to the Dawn, before Lorkhan tricked the gods.
And according to MK, they are not about half measures :
"To kill Man is to reach Heaven, from where we came before the Doom Drum's iniquity. When we accomplish this, we can escape the mockery and long shame of the Material Prison.
To achieve this goal, we must:
1) Erase the Upstart Talos from the mythic. His presence fortifies the Wheel of the Convention, and binds our souls to this plane.
2) Remove Man not just from the world, but from the Pattern of Possibility, so that the very idea of them can be forgotten and thereby never again repeated.
3) With Talos and the Sons of Talos removed, the Dragon will become ours to unbind. The world of mortals will be over. The Dragon will uncoil his hold on the stagnancy of linear time and move as Free Serpent again, moving through the Aether without measure or burden, spilling time along the innumerable roads we once travelled. And with that we will regain the mantle of the imperishable spirit."