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I would go with the Special/Physical split from the 4th generation games mainly because it drastically changed the movesets of some Pokemon. The change brought new moves that some Pokemon can use more effectively like Flare Blitz for Arcanine. Arcanine lacked a decent STAB attack from the physical spectrum until D/P/Pt came around.
i love the two on two battles. because they are actually double the fun and double the moves and everything double =/
some attacks might hit you all and some might hit just 1 of the 2
thats what i like at two on two