CLI is certainly possible but you have to convert it to Wireshark format with a perl script.
I have 5.2 GA on a FortiGate 100D and also on FortiGate VM and this options is there for me (see pic).
Also don' t forget you can capture packets on a per-rule basis now! Can do this one from GUI or CLI. In GUI there is a checkbox, in CLI there is option under rule edit for set capture-packet enable/disable
Sean Toomey, CISSP FCNSP
Consulting Security Engineer (CSE)
FORTINETâ€” High Performance Network Security