LOL...I know. I'm hoping you guessed that it wasn't the most serious idea for a storyline. I was just doing WWII at school and posted that for fun.
As for a sophisticated idea:
An extremely long game. Not sure if this would be humanly possible for times sake. Map based purely on Great Britain. you start of in you home town of Thame (little outside Oxford). You have a big brother/sister and they want to become champion like you. You have a choice of the Kanto starters and your brother/sister will choose better type poke as per usual. You go from town to city to town via motorway which are shortened bike paths (without the slope) with Bikey Gang and Cyclists and defeating gym leaders and trainers along the way. The evil team is Team Terrorist. They plan to steal pokemon and ransom them but you always thwart there plans.
Towns/Cities included (no particular geographical order):
After you have travelled to these cities/towns, you surf to the isle of man, and take a trick route with many high leveled trainers and some rare pokemon (not legendaries...yet). At the end of this route (its basically victory road), you sail on the Queen Mary II which has lvl. 55is poke trainers of all sorts, and then you dock at Dublin and battle the British Quad. After this, legendaries are set free PURELY to complete you pokedex and have fun.
PS I know this is rubbishy because of the legendaries but I find that having them against Elite Four is boring first time.
PPS This is Kanto dex apart from having eggs of all pseudo-legendaries outside kanto (Larvitar, Bagon, Beldum snd Gible) collectable from certain NPC. Only one can be chosen before first battle against 'British Quad', and then others after each other time.
PPPS I know this sux.