OK, so this is easily-enough explained now...
1. Flat-file backups like databases allow a tape drive to run at up to the fastest speed it can. There is no interruption in the data being streamed from disk to tape. So throughput is expected to be much higher.
2. Having millions of small files creates a stop-start effect on the tape drive. It writes a file of a couple of MB, waits for the next file which it writers, waits for the next file which it writes etc. Data that isn't streamed fast enough or consistently enough means the drive has to wait. Read below for a detailed explanation:
http://searchdatabackup.techtarget.com/definition/shoeshining-or-backhitching
3. Using fibre channel in this type of configuration won't help you unless you utilise the ESO option of BE 2012 and invoke SAN SSO (which means you need to have Backup Exec 2012 installed on any other remote servers that have access to the SAN). You'd end up being able to stream these servers directly to the shared tape library (which you say is FC-attached) at much higher speeds than the LAN. Read below on this:
http://www.symantec.com/business/support/index?page=content&id=TECH196579
http://www.symantec.com/business/support/index?page=content&id=HOWTO24287
Give those a read...
Thanks!