Character-wise, I'd say it would be Alder. Cynthia and Morimoto were bonus bosses so they weren't supposed to have backstories and stuff. Ghetsis was a complete monster and I hate him. Alder was the ONLY Champion to have actually attempted to fight the leader of the evil orginization, whereas the other three just watched. Also, he has a cool story. : D
Battle-wise, it would be Alder again, because at least he doesn't rely on haxx, like how Cynthia does.
If you people are going to rant about Alder having three bug types here I suggest you look at Steven's team. He has THREE Rock-types and THREE Steel-types (there is an overlap with Aggron). And let's not talk about Lance.