I am biased against FCoE because it’s too new to be blithely and broadly recommended for production enterprise use. That’s all. Yes, the standards are standardized and there are products extant. But that’s not enough for me.
iSCSI is an excellent choice in situations where Fibre Channel investment is nonexistent or badly in need of wholesale upgrade. FCoE, on the other hand, is likely to take over in high-end enterprise shops. It is relentlessly promoted by major vendors, and it seems that they will force the upgrade eventually.