My org presently uses OpenCTI and a Call Center.  According to the release notes, Call Centers are not supported in Lightning, and indeed, the Call Center functionality disappears from Setup when Lightning is enabled.  This makes sense, because it is unclear how or where an OpenCTI softphone would appear in the Lighting UI.

But, what is the plan for supporting soft phones / OpenCTI / Call Centers and Lightning in the same org?

It looks like we either give up our softphone functionality or enable Lightning, but not both...thats an upgrade blocker!