I'm currently playing in a D&D Shackled City campaign.
One problem is planar travel, as someone alluded to earlier. We also frequently use things like speak with dead and divinations that keep us on the trail of the BEGs. Without these, I think you'd have to come up with some other way of getting info to people and for travelling. They could travel the conventional way, but you'd have to allow for more time in the plotline because they can't just teleport from one town to another.
Apart from that, there's Skie's and many other magic item shops that play a part in the plotlines. Somehow, the PCs would still have to go to those places periodically to keep involved.
That's all I can think of at the moment. As Odhanan said, the PCs should be about as powerful as D&D PCs with proper magic item equipment, but in different ways (like no scrolls of teleport).