The fact that you are working with 50+ tracks has nothing to do with your audio interface, or USB vs. Firewire. The Duet series is only capable of a few simultaneous tracks in and out- and both USB 2.0 and Firewire have plenty of bandwidth to accomplish this. I would go with the Duet 2- because it's current, and has the best chance of being supported by Apogee long into the future (drivers, etc...) There are some other advantages to the Duet 2 like higher sample rate, etc... the advantages to the ONE is the built in mic (if you need that)- the Duet 2 has 2 built-in pre's though...
http://imsproav.com/main/APOGEEDUET2.html
Feel free to contact me if you have any questions about this...