McData 4500 and Brocade 5300 can be connected together, just need to make sure proper code and interop mode is set on each switch. Before you even consider that route, consider this:  In order to perform LAN free backup you have to have either fiber channel tape connectivity directly to the system that needs to be backed up or utilize array snapshot functionality where you take snapshot of host production LUN, mount it on backup server and then spin it to tape. For example for exchange and sql EMC sells Recovery Manager that puts database in "consistent" mode, initiates snapshot, puts database back to normal mode. Snapshot gets mounted on backup server and then you spool it to tape.  Some backup applications sell "storage agent" license, i guess it's kind of like your media agent license. It allows you to present shared tape resources, for example to your exchange server. So the storage agents talks to your backup server and negotiates tape resources, once resources are obtained, it sends data traffic over fiber channel and meta data (control traffic) over IP.
I have been told not to connect our 2 FC 4500 switches to our newer 5300 switches. But when I backup from the newer san CX4 to the older San CX500 that connects to Commvault everything is going over the network. We are using Commvault 8.0 and I am trying to find the best solution for this bottleneck. Not sure if I should build another media agent attached to both sets of switches, or to somehow Isl switches together without the older 4500 sw's taking ownership of the newer 5300's.
Connecting 2 sans