Well, now the Rockets have stopped working with us we only have two other choices if we want an alliance with another team: Those Insane Guys from Sinnoh, or those new knight-guys from Unova.
Also, if you want a Professor that knows a lot about legends, I say neither Oak, Elm, or Birch and instead capture Rowan. He's only famous locally and the only person who would notice his dissappearence would be his aide. And maybe Oak.
UPDATE:
According to our "old friends" at Team Rocket Mr. Pokemon, a man who is a friend of Prof. Elm's and lives outside of Cherrygrove City in Johto, has the two orbs.
ANOTHER UPDATE: All three legendaries, Rayquaza, Groudon, and Kyogre, have been spotted by the ancient tower on Route 48 in Johto. This information was gathered by yours truly, and provides further proof that we should set up base in Johto. Then, after we get Kyogre, we can finally settle who gets Goldenrod.