I'm wondering if the problem with SC is it needs to know that Kore is installed, perhaps manually installing it is bypassing whatever it is that flags it as installed for SC. An alternative approach might be to fool the installer into thinking you are on an earlier Mac version: https://www.reddit.com/r/apple/comments/3r0v8w/how_to_change_your_osx_version_number_to_bypass/
Could be, that running the installer means some juju that didn't happen. I have seen this trick, but it was a less involved version which did not mention having to go back into Recovery Mode to set the version number back to reality because you can't even use Terminal on the loaded OS it's so borked now. That seems extreme. I deleted the Kore 2 installer, I'm not sure I want to push this further. As if it's just restin', or it's pinin' for the fjords. Instead of having joined the Choir Invisible as every sign shows here. Beautiful plumage, innit.
As to USB, I just bought a keybd controller and it plugs and plays with no issue (or drivers). Line 6. So, there is no 'USB killed by El Capitan' per se.
UPDATE: In the installer Package Contents (installer for v. 2.1.0.009), I did the change (in distribution.dist) "my.result.message = 'Installation cannot proceed, as not all requirements were met. This product requires at least OSX 10.4'" to "... at least OSX 10.04" and the installer finished; I ran standalone, Activate; Service Center recognized it, I activated; now downloading updates in SC. I had this nagging memory of actually loading Kore 2 in Studio One 3 and Cubase 8.5 back in December, from whence I do not remember any activation issue, which is weird. My recall of what I did or didn't save in these two hosts is fuzzy but I think I'd remember this hitting a wall as well as numerous run as demo stalls. Kore 2 working and activated in OS X 10.11.4 here now.
It was pretty flaky as far as what showed up in the list, such as it sees VC 2A and VC160 but not VC76 AU.<-my problem. Saw vsts for a couple of things but not the AU. Maybe restart the damn machine and it will wake up and smell the coffee. But, such as working with Massive will be MUCH easier in Kore with basic controllers showing up needing no digging. So I'm glad it works. i never bothered with Absynth 5 in it really, I found (everybody else knows this of course) that saving ksds at a higher level than A5 resides works, the whole .nabs problem doesn't stop that. It not seeing Reaktor 6 is a drag, if that keeps up. NB: I'm an idiot^, I forgot the day before setting it to *run as 32-bit*. I'm now sure it was working in December. I definitely had it going longer than 15 minutes, and I know I'd remember the whole problem. I don't know why the difference.
It should see R6 - I'm on El Cap too and it does. Try going into your database cache and trashing any Reaktor 6 related ksds, then rescanning.
So, I'm new to R6 and evidently there aren't any .kds but the usual suspects, there is no Reaktor 6.kdb at all so that's a washout. I copied/pasted Reaktor 6.vst into Kore 2 Plugins and it doesn't see that. OMFG. This is insane. I launched Kore 2 to have another look, and it is not activated, Service Center does not see it, NA does not list it (after it did). EDIT: I DON'T advise to run it as 32-bit
To install in OS X 10.10 and above, R-click and Open Package Contents; see 'distribution.dist'; now replace the 1st 11 lines (the last is empty) of that file with the above