I choose the latter. I don't really like having all these colored teams - Blue, Gold, Red - as isolated plot streams. We can have the colored teams, each with its own leader, but they should be sub-teams under the main banner and they should all interact with one another frequently. For one thing, if something particularly cool is happening with, say, Kitty, or Rogue, we can touch on it each week. We don't have to wait a month.
Each sub-team would still have its leader. But above them all would be the overall leader of the X-Men, who, in my opinion, should either be Jean or Storm. I think Jean might get the immediate obedience a split second more quickly, but Storm is probably the better leader, because her instincts are broader. She's been a vigilante, a thief, a goddess, and a queen. She brings more to the table. Plus she combines a potential for ruthlessness like Scott with a fierce maternal protectiveness like Jean. Also, minus the Phoenix, Jean just isn't as scary as Storm, and the overall leader should be a little bit scary. If Wolverine gets out of line, Storm could (and possibly would, given the particulars) leave him a smoldering husk on the beach to reconsider his approach to life.
Multiple X-Books or Weekly X-Men comic?