So, I've read all the posts here, researched other forums, and (with an electronics background) was still struggling to understand why the neck/middle pickup combination was so weak compared to the other 4 switch postions. It seemed that the only reason the output would be so weak for the combined neck/middle pickups would be if they were out of phase. I found a wiring diagram for the JTV-69 pickups, checked my guitar, and everything was per the wiring diagram (note that the board the pickups are soldered into, has clear markings for each lead, and of course the pickup leads are color coded black and white). So today I reversed the leads of the neck pickup, reassembled the guitar, and guess what? Normal and expected response from all pickups and combinations. Now the neck/middle pickup combination has normal volume, and the "quacky" midrange tone you expect. My only explanation is that the neck pickups were manufactured with the color-coding on the leads reversed. I know this same issue has plagued many other JTV-69 owners, so don't know how many guitars were manufactured with this issue, but for those of you that are suffering the same problem, now you have a solution.
Line6 JTV-69 Pickup Wiring.pdf