One of the challenges, especially for mission-critical or performance-sensitive applications, is that there is higher latency in iSCSI. Specifically, wrapping SCSI packets around TCP/IP protocols has some overhead. It is also difficult to guarantee the performance of mixed networks. For example, if your VoIP, iSCSI, email and Microsoft Word documents are all on the same wire without some form of quality assurance for performance, it's difficult to guarantee it. That's one of the nice things about Fibre Channel SANs. It's almost guaranteed there won't be any other traffic except disk traffic on that network.
Listen to the iSCSI vs. Fibre Channel podcast here.