You can't fix a hardware problem with a software solution lol.
I think some users, along with the media (honestly the people who review stuff nowadays are kids with little to no engineering insights), are just as clueless as HTC when it comes to the M9. What saddened me (as a lifelong HTC user since the HTC diamond), is that they never formally admit to the problem, and throttling a next-gen chip to the level of its predecessor is not what I would consider fixed.
Just about every SoC in phones throttle to a certain extent after thermals reaches a certain point. It is certainly nothing new, Qualcomm indeed does run hot, however, HTC has optimized how/when it throttles. I suggest you read some more articles to brush up, starting from some AT updates about the phone.
One thing of note, the Z3+ and the XiaoMi Note whatever, is running an "updated" Snapdragon 810 v2.1 that is supposed to have a much better thermals, and Xiaomi also has thermal patents specifically to address the 810. But upon released, their phones hit around 60C. Which is a far cry from the original numbers.
Take away from it what you will, but from initial numbers from a few sites, after the fix, the benchmark numbers was bumped up a bit, while also running cooler. So IMO, kudos to HTC for following up and trying to rectify the situation, even though there are people who continue to spread FUD.