Hm, wasn't the best warstory; I think the main problem I have is that you missed out one of the most important parts - choosing which four Pokémon to use. You haven't even mentioned what the other two are! VGC teams consist of 6 Pokémon, and battles can be won or lost based on which four you choose and which you choose to lead with. I'd have liked to have seen all six from both sides protrayed at the start and your reasons for why you went with these four (and those two leads) as opposed to which four you predicted your opponent to bring.
Other than that, a decent battle, though you did seem to have the upper hand throughout. Running both substitute and protect on two of his Pokémon seems kind of odd. And I'm not really a fan of double protecting to scout fake out - sure you save yourself some damage, but you leave your opponent totally free to set up, as indeed he did do here.
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