Difference between ISL AND dot1q :
(1) Network Overhead. dot1q has less network overhead than isl. dot1q encapsulates the header of the frame while isl encapsulates the entire frame.
(2) Native VLAN. In dot1q, frames sent across the trunk doesn’t have a header. The remote switch will assume that any frame without a header is destined for the native vlan. In isl, every single frame will be encapsulated, regardless of the vlan it’s destined for.
(3) isl is Cisco Proproetary while dot1q is Industry Standard