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Battle One:

Who can destroy the most of the omniverse the fastest.

And then rebuild it? Based upon feats only.

Battle Two: Head to head on the count of three. They duke it out.

Well Pre retcon MM did (when he was angry IMO) slag billions of universes but a Omniverse is infinite more and Merlyn has fused all the life energy of the Omniverse into crystals that he can break at the same time with basically a thought so I think he is the One of the two that can destroy the omniverse fastest.

Rebuild it would be MM, be repaired all the damage Beyonder and him caused, with a wave of his finger. And Merlyn hasn't really shown any Rebuilding feats According to my knowlegde.

Molecule Man for the win here IMO.