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Is there a way to make controllers to deform some specifics vertices like they would act in proportional editing? ( no shapekeys )

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That is essentially what bones do when deforming a mesh via vertex groups: each vertex assigned to a group named after a bone is deformed by that bone with a factor from 0 to 1.

You can edit that in Weight Paint Mode or in Edit Mode.

You can't change the weights across the animation. But you can have one bone controlling several bones via constraints. The target bones affect specific areas of the mesh, and you can animate the constraints' factors to animate the area of effect of the main bone.

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