Yeah, Bomber and I did well as double PT. We pretty much crushed everyone except for skilled ranked players. As far as our best lineup, it would probably have to be Charizard and Squirtle, ie the two we start with. Water Gun to Rock Smash is raaaaaaaaape. Charizard does well in doubles provided your teammate doesn't allow him to get double teamed, and Squirtle's great at applying pressure, thus making it much more difficult for the enemy to focus all their efforts on Charizard. I don't even think our Ivysaur got gimped at all. Bottom line, two PT mains know the weaknesses of their characters and are great at covering them in doubles.
I've also teamed with a Wario before in doubles, and Toby is right. Wario makes for a great partner. Like Squirtle, Wario's great at pressure, so Charizard can't get gangbanged. With timing, Wario's fthrow to Rock Smash is really, really good, and enemies don't see that coming, haha. Wario hates being grabbed, but in doubles people have a harder time grab releasing him with a partner roaming around, so Wario makes for a great doubles partner with lots of characters, really.
Although I haven't teamed with my friend's Ness in a tournament, Ness and Charizard work well, too. If Ness gets weak, just Flamethrower him. Heals him really fast.