Ports vs The Logic Board
If anyone's seen the tear-apart photo's of the new model (Sorry, no link handy) you'll notice that the ports go the entire length of the logic board along the side. Because of the removable HDD and long battery along the front, there's no way to put ports on the front half of the computer. The right side is completely taken up by the optical drive. I think that explains the choice to use the Mini-Display port as opposed to the full sized port: to actually fit everything that's on there. The same goes for the FW400 port. If you added those two ports on (to the left), you wouldn't have any room to put the hard drive there. The only way to physically fit more ports onto the machine is to a) make it bigger (depthwise,) which it seems people are complaining about, or b) abandon the way all Apple's notebook screen hinges work -- covering the entire back of the machine. It's all a trade off. The easy access HDD/Battery for the room for ports. According to Job's keynote, the HDD was one of the most asked for features.
One of the things Apple did drop the ball on though is the resolution of the screen. If Alienware can come up with a 1200 vertical line 15.4", (as a BTO) why can't Apple? In this case, I think the focus was being "Green." The Alienware's still use CCFL (and glossy one's too.) But I think the glossy argument has been beat to death.