I just chatted with Apple tech support about this issue (Robert was awesome, btw - case #686703003 in case anyone from Apple reads this). The only thing we really did was to confirm that it was set up correctly and then to log out of iCloud on my MBP and then back in again. Since then, it's been working fine. Even without being paired, continuity features now work and even SMS forwarding works fine as well.
I had upgraded from Mavericks to Yosemite and then connected my iPhone 5 to my MBP and set up continuity on it once I'd upgraded to iOS 8 (and then SMS forwarding when I got iOS 8.1). My iPhone 5 had been paired with my MBP. When I paired my iPhone 6, I removed my iPhone 5 but it was still listed in the system report. I also removed my iPhone 5 from my devices on iCloud as well. Once I'd logged out and back into iCloud on my MBP, the reference to my iPhone 5 in the bluetooth section of system report was gone.
My iPhone 6 is now working as expected with all handoff/continuity stuff even though it isn't currently paired with my MBP according to the bluetooth control panel. It shows up in my wifi menu for auto-hotspot as well.
So, if you haven't already, you may want to try the following:
Make sure both devices are connected to the same wifi network
Both devices are signed into iCloud
Your mac has handoff support enabled (system prefs > general)
Your iPhone has handoff support enabled (system prefs > handoff)
Log out and back into icloud on your devices
Hope it works for you guys as well.