Rainer Brockerhoff's studied dissection of the new MacBook's design—how certain design choices intersect with the realities of components to produce real notebooks—perfectly explains how they are not simply a wishlist of parts and features that magically come together. There are always compromises.
The unibody construction, along with the decision to make the hard drive and battery easily accessible essentially determined the rest of the internal layout, and you wind up with motherboard that doesn't span the length of the notebook. So, all of the ports have to go on one side, and the limited space means you get three.
Apple chose Ethernet and two USB over, say, a combo with FireWire but no Ethernet. These design principles apply to every notebook, so it's worth reading if you've never thought about how the bucket of parts in your lap comes together. [Rainer Brockerhoof via Daring Fireball]