For ISL's, if the line card is gen2, it must be configured as dedicated. For the port mode, I would recommend that you hard code the mode to E. I also like to code the speed on ISLs so that there is no chance that they would negotiate to a slower speed. IE: you don't want to have a 2GB link negotiate at 1GB.
As for storage controllers, depending on the fan in ratio, I would recommend hard coding them to the device speed, and if the port-group has the bandwidth available, make them dedicated.
As for hosts, they should be on the shared port, and I would leave them as port mode = auto. This way they can negotiate F or FL. You might want to configure a 'maximum allowable auto speed setting'.
IE: if your hosts have 2GB HBAs, and are plugged into a 4GB capable port, they will never negotiate to 4GB...so why have the MDS think it needs to keep some bandwidth for that port (in shared mode). I forget the command, but there is way to set auto-max for the port speed on shared ports.
Hope this helps,
Mike