Good question. For me they would be:
The Black Widow. Marvel needs to push more women into prominence and Warren Ellis proved in his Secret Avengers run how intelligent she can be.
Spider Girl. Bring back May Day Parker! Have her travel back in time or something, wind up in the 616 MU. Have her team up with Anya Corazon and call the title Spider-Girls!
Jimmy Woo. I loved Agents of Atlas and I would love to see those characters return in some capacity. Jimmy Woo as the leader of one of the world's most powerful secret organizations should be a prominent member of the MU.
Those are the only three I can think of off the top of my head.
Whatever happened to the Agents of Atlas? They seemed to be a good following for a brief moment and then they just went away