The downside with the PCI-Express route is that waiting for it is going to take forever. After all, when PCI-E is out, you'll simply *have* to wait for the BTX mobos and cases, and will *have* to wait for that new generation GPU, and that new 64-bit core stepping, and that, and that...
Just buy what you need, and you'll get a great computer. Wait a while, and you'll regret it anyway, no matter what you bought. It's the way of the computer.
