Suggestions on a campaign for a new player?

[Galt_Devil]

So, myself and a very good friend of mine have done several several tabletops together. I recently decided that I want to run a DnD 3.5/PF game for himself and his younger brother, and maybe another young friend. It would start at level one, and probably be a generic dungeon crawl until somewhere from level 5-7, at which point I want to start throwing them into a real important storyline. It doesn't need to be Game of Thrones intrigue, but I don't want it to be a stereotypical Good Faction vs Bad Faction either.
Any suggestions?

[Yora]

You could do something with three neutral faction whose each have a different plan that goes in the way of the other two. The PCs could decide to side with either of the faction or to remain neutral and protect those caught between their wars with each other.
They could either decide that one of the plans is a good one they want to support, or than one is so terrible that they will help one of the other groups to prevent it.

The Witcher has a war between human knights, who protect innocent humans, and nonhuman rebells, who fight against their opression by the governments. Many of the rebels do pretty awful things to humans who didn't do anything when they attack their targets, and the knights are not particularly mercyful either and with their actions help maintain the suppresion of the nonhumans.
In Dragon Age, you have the Templars, who police all mages, because mages can become possessed by demons and turn into dangerous monsters when they experiment with dark magic. But this means that they don't give mages the option not to be part of the official guild and many of them take no chances and kill mages who try to escape, even when they have not yet been possessed by a demon. And this of course makes many mages want to learn new magic which they can use to escape, which is usually dark magic that attracts demons to them, and almost all mages that do become possessed are in just that situation. You have the Templars, who hunt rogue mages and control that the Guild Mages do not learn dark magic; and Rogue Mages, who usually hide from the Templars but sometimes try to help Guild Mages escape. And then there is the Guild Mages of which some want to stop the Rogue Mages so the Templars can ease down and don't need to be so radical, and others want to defeat the Templars and join the Rogues.

Just think of something where you have three groups who have good ideas, but sometimes do bad things to the other groups because of it.