We've finished preliminary testing with Indigo 6.1.4 on the GM candidate of El Capitan. On a MacBook, everything seems to run correctly. The Insteon PowerLinc seems to work well as do both the Z-Stick Series 2 and Gen5. We haven't tested any other Z-Wave interfaces since they aren't officially supported, so YMMV.
We do, however, have some other news: on a Mac Pro (early 2009), things are decidedly not going well.
Our testing shows some extremely bad behavior on the Mac Pro. If you plug a Z-Stick Series 2 (not the new one) directly into any of the USB ports on the Mac Pro, the Z-Wave interface will hang up very badly - in fact, it will hang up such that the Indigo Server will not restart without rebooting your Mac. In an interesting turn of events, we plugged the Z-Stick into a Dynex USB hub, and it works correctly. This of course goes against the conventional wisdom that you should plug interfaces directly into the USB ports on the Mac. We believe it might have to do with how the Mac Pro tries to detect USB 1 vs USB 2 devices, but that's just a guess.
Another problem we experienced on the Mac Pro is that the PowerLinc would, every couple of days or so, appear twice on the Mac Pro's USB bus (as shown in the System Information app). When this happens, communication will never work and a reboot is also required. These two problems together seem to indicate that El Capitan has some issues with USB on Mac Pros (at the very least), and we highly recommend you avoid upgrading if that's what Indigo is running on for you.
One final problem we found on the Mac Pro, which is completely unrelated to Indigo, is that multiple video cards (to drive multiple monitors) causes El Capitan to periodically (about every 5 minutes or so) crash out of the Finder back to the login screen. After reporting this bug to Apple, it was marked as a duplicate of another bug, so clearly this is something others are seeing as well. Unless Apple fixes this, then if you have multiple video cards in an older Mac Pro, you will likely need to remove all but one to get the thing stable enough to use.
As always, we highly recommend that anyone with the option wait on the upgrade until at least the first bug fix release has dropped (10.11.1). I personally, being the one with the Mac Pro and all of the bad experiences, would wait for several bug fix releases before upgrading. Again, do so at your own risk and YMMV.