I like Erik's comments about the Elf/Orc war. It's old-school D&D, and the idea of throwing "prince Melf" into the mix - that's awesome. I'd totally jump on that - it'd give my brother a chance to play a Duskblade (old school D&D elf!), and that Dwarven Defender my friend's been thinking of playing.... geez, it'd be perfect.
I do like the idea of throwing in "mini-campaigns". I think, after Savage Tide is over, you guys should just spend a year or so playing with 3-part adventures, or even 6-part adventures (a 6 parter would be pretty cool, I think).
The idea of two BBEG who hate each other is kind of cool. It reminds me of the latter levels of Halo 1, where the Flood is one faction, the Covenant is another, and the Sentinels are a third; as you move through parts of the game, you can see these factions involved in a war with each other. I think, on a larger scale, that might be a cool idea for a game.
An example of that, going with fiends (since it seems EVERYONE loves the idea of outsiders in an AP), you could have the devils and demons in a war with one another (I believe it's called a.... blood war....?

). The PCs don't really care about who wins; they have their own goals, but to get to them, they have to deal with these warring factions.
Finally, as one last note - why not run an AP based around Carceri? I think a really cool AP could be built around the idea that the PCs start off as criminals who are sentenced to exile on Carceri (at first level, no less!). Then, they have to survive with the group they were exiled with- mostly thieves, orcs, and murderers. The whole point of the campaign is trying to escape Carceri.
Or, to take that idea a bit further.... the PCs start off in their city (Greyhawk!) where they are trying to fight some villain or another. They find that the villain has plans to destroy the city (Gadzooks!) and, along the way, get framed for a crime. They know the villain is responsible, but cannot prove it, and so are sent to Carceri (5th level or so). The next 10-12 levels are spent trying to get out of Carceri, dealing with nomadic tribes of good prisoners that have been stuck there forever, and all sorts of evil critters. THe last 3 levels consist of getting back into the city just before the villain enacts his evil plan, and trying to stop him.
Just an idea.