Not really, you're fighting on the same campaign map from different sides and physical start points, it's a Total War game, it's very light on story and I don't think any of the win conditions present in the game actually happened in the fluff*. I think that kind of like the other TW games that I've played, the challenge is to do what didn't happen in reality/fluff and actually achieve total victory.
You'll find lots of weird non canon shit happening. My first game as chaos I started storming South to find that the wood elves had managed to conquer pretty much all of the Empire North of the River Talabec, excepting Middenheim and Blood Keep and a good chunk of the land South of Nuln. They had already done my job of wiping out Brettonia for me.
I just went with personal preference.
*I should point out that Storm of Chaos was the last point I paid real attention, The End Times can fuck off. AoS doubly so.
EDIT: As mentioned above, empire and dwarves are probably easiest. Orcs and Vampire counts have mechanics that make them a bit trickier to play, but only marginally. Chaos is probably the hardest due to being a horde faction.