I’ve had a similar problem and just got it fixed last week. 2nd gen pro 12.9. It might not be your same issue, but it sounds like some people are mentioning what I had.
For me, over time the touch input would occasionally respond intermittently but the pen always worked. I waited a few weeks or months, updated the OS, tried a reset, etc, but it was still there.
I took it to the apple store and was worried I wouldn’t be able to recreate the issue, since it was intermittent, and that they’d give me the run around.
But I started explaining the problem and before I could even finish, the employee pointed out that he could see the backlight shining through from the edge of the display. I hadn’t even noticed it, but once he pointed it out it was definitely visible. He said sometimes the glue used on the screens can have problems over time, which can cause the screens to separate and lead to touch response issues.
They replaced it immediately, I was very pleased, I had forgotten how responsive this iPad can be. I do have AppleCare, but they should replace it regardless, if this is your issue.
Good luck.
[doublepost=1528005803][/doublepost]I should have gone to the Apple Store much sooner. If there isn’t an Apple Store near you then call Apple. Just do it.