ISL is Cisco specific, 802.1q is open so you will be able to use it with different vendors switches as well.
With ISL, traffic from all VLANs is tagged whereas with 802.1q the native VLAN is untagged. This untagged traffic can lead to problems if all switches are not configured to use the same native VLAN.
It used to be that ISL could be used with PVST and 802.1q couldn't. This is no longer a restriction.
Personally, as long as you are prepared to take the care with the native VLANs, I would say to go with 802.1q - in that way if further switches from other manufacturers are added at any time you will be OK. There are also Cisco switches that are unable to run ISL, so again 802.1q is the only option if you have one of those.
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