Actually I don't think they wanted to capture the legendaries for themselves, they just awoke them from their years-long sleep, causing them to tip the balance between land and sea. So I suppose, here's one example that the Team *weren't* trying to capture the legendaries? Basically Team Aqua were all about "the sea is awesome so we should make it bigger" and Magma were the opposite. Groudon and Kyogre are legendary Pokémon, so there is no way that they could possibly be tamed, unless of course, you happen to be a 10 year old boy/girl who through some crazy sequence of events (delivering a letter to Steven!), happened to be there lol ;)