Meowth doesn't need to be Team Rocket's. Granted, maybe a SSBB Meowth should reference Team Rocket's Meowth in some way or another, but there's no actual need to make it the exact same individual (it could be given Pay Day, etc.). And yes, Pay Day is signature of Meowth. Other cats may learn it, but it's via special ways, namely Pokémon Box: Ruby & Sapphire.
Plusle would most probably be the default leading one if allied with Minun, because Plusle is often mentioned first and its Pokédex number comes before Minun's. But they could be shifted either in the selection screen, via a special move, or by a button combination prior to the battle (think Zelda/Shiek). Their stat differences could be given emphasis this way.
Guys, don't worry about 2G at all. Why worrying about having a representative from every generation? 2G was a short generation, and that's why it's natural to have so few candidates from there. Scizor would go for suitability, but that's not enough. I wouldn't hesitate to mention Wobbuffet, Togepi, and Marill if there was a need for flagship 2G Pokémon characters, but they're no longer that important (and Wobbuffet would be hard to implement). And there's still Pichu if they resist to remove it (they need to IMO).
To the Shiftry suggestion, remember this Pokémon had a counterpart in the same generation, which was Ludicolo. From what we've seen, the only time they included a Pokémon species which had a counterpart, it was Jigglypuff (vs. Clefairy), but Shiftry isn't a recurrent animé character, unlike Jigglypuff was.
My answers in threads like this one are typically based on the number of Pokémon I believe could be playable in SSBB. Being Pokémon such a big franchise, it could be assumed this number could increase from SSBM in the same ratio as the total number of characters. My bet is they could easily include a big total of 6 Pokémon this time, with Pikachu, about 3 kickass legendaries, and about 2 Pika-friends.