I personally like both characters but if you were to choose between who to have as your Warchief would you have Baine or Thrall? I say Thrall only because we need stability and peace and somebody to ready Baine for the job someday as I think Baine just isn't ready yet.
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Baine and Anduin being faction leaders would make the game World of Peacecraft And please, some love for Zekhan
On another note, regardless if Baine and Anduin are leaders of their factions I don't think that means a guaranteed peace between their sides. Honestly I think they're setting things up so that not all the leaders of the Alliance and Horde are for peace. Prime Example: Tyrande