No catch. It's just a newer card interface system. It uses more lines to communicate with more parts of the computer separately so that everything doesn't have to share fewer lines. PCI-e is going to replace normal PCI slots, as well. There are different speeds, and the higher the speed, the bigger the slot. Currently, PCI-e comes in x1, x2, x4, x8, x16, and x32. Most add-on cards will probably only need x1 or x2. Graphics cards obviously send and receive a lot more data, so x16 is the standard for gfx right now.
Overall, it's WAYYYY better, faster, and more efficient than the normal PCI/AGP architecture. If you're getting a motherboard, PCI-e is highly recommended. Even if you don't plan on upgrading much, the price difference between a PCI only motherboard and a PCI-e equipped motherboard is nominal. Go with PCI-e.