Groudon, Kyogre & Rayquaza -> bad, bad idea. I mean, the changing weather is just so confusing @.@
Mewtwo, Lugia & Ho-Oh -> not bad, mewtwo and lugia are just great.. but Ho-Oh, I love him for his looks, but he is too fragile >.>
Now.. Dialga, Palkia & Giratina vs Reshiram, Zekrom & Kyurem..
I would choose Reshiram, Zekrom & Kyurem, simple because I like their typing and looks more xD