Hey Seth,
UNI? :) I'm from Iowa originally, so that's what I'm guessing since you said you're at a university. Anyhow, my first question is what's the hardware configuration like? What kind of network, server, hardware are you running on?
I only ask this as we just upgraded from what used to be the top of the line hardware in it's day to some new HP DL380 G5's with SAS SFF drives at 5x146GB RAID 5 at 10K on a 1GB network. These are our file redirect servers which have 4 data volumes each with data such as what you listed below and ranging from 400-900 thousand files each. We went from approximately 3-4MB/sec (compressed) on our full backups to 11-12MB/sec (compressed)! We did some tests around this finding and it was 100% hardware in our case that bumped the throughput (SAS drives being the key--not to mention a fresh set of data laid on the drive with no fragmentation--which we plan to maintain going forward).
Anyhow, back to your original question about the Flash Backup option. I just got through testing it for a couple of clients I have with 50 million 1k files on a single volume. The backup worked well getting me up into the 5-6MB/sec range, but I couldn't get a restore to work for the life of me. I went up to 4th level support with Symantec, but basically got nowhere. It sounds like there's already another issue out there like mine that engineering is looking into, so I'm holding off for right now. Bottom line, test backup and restores when evaluating flash backups.
That's all I've got for now!
Lance