due to the way apple set up the hard drives in the new mac pros I don't see a reason to go external other than maybe if you needed to grab a drive and go to another location...the easy plug and play of the new drive layout is very nice and easy to get to. Plus with 750gig drives you can get a lot more space than you would ever need, unless you are doing video...
If a Mac Pro is in budget then thats the way to go, the storage is way cheaper per GB and the bandwidth is almost 8 times as much a FW400. With 4 swappable trays it's not a million miles from external. Cheers