I just want to face the Lucky Charms mascot as the final boss battle.Well the way you said it makes them sound like Leprechauns (Which is still fitting, but it will require us to give them an Irish Accent) but I like the idea
And then punt the little bugger off a cliff. They're my Lucky Charms now.
More on topic, it'll be rather difficult to make Team Luck-Sack unique in its own right. As much as they are supposed to depict all the strategies that Smogon frowns upon, it would be shallow and uninteresting to just inordinately bash a group of nondescript grunts for it.
Perhaps, to give the storyline some depth and perspective, we create a character that is somewhat of an analogy to N in the BW games. I propose a character, most likely physically younger than the main protagonist, who was born with the world's most coveted treasure in his mind: The One True Balancing Solution for All Pokemon. So earth-shatteringly powerful is this knowledge, that this poor child must pay the price by being unable to walk, bound to a wheelchair for life. He also cannot utter the entire One True Balancing Solution for All Pokemon in full, because when he utters but a few words of the Great Truth, he simply passes out, too frail to handle such a burden on the mind and body.
However, due to the collaboration of several powerful men, embittered by the rules of Smogon and enamoured with world domination, the young boy's words have been misinterpreted and misconstrued as 'freedom of usage for ALL moves and strategies', and hundreds, if not thousands, of people that feel just as embittered as the puppet-masters behind it all, join Team Luck-Sack, unaware that they are merely forwarding a few men's dreams of turning the world upside-down.
To connect this to the first town, perhaps the very last NPC you meet before moving on to the next route is a rather silent boy in a wheelchair, forlornly staring at the tall grass and ponds, before slowly pushing himself back home into one of the houses in the first town.