More rumble would mean more battery, and people consider Wii U pro controller so much because of the battery.
About the analog triggers: this would mean a revision on the gamepad too, and i'm betting nintendo is not willing to make this big change in a so expensive controller.
About the audio jacket, if nintendo didn't care about making a in game chat system on the machine, imagine yet making a phone jacket avaiable for a alternative controller.
About the shortages, its simple: reatalier alreadly have enough trouble making wiiu avaiable, alternative controller are even worse, they jsut doesn't bother anymore.
This means nothing.
"Hardware design isn’t about making the most powerful thing you can.
Today most hardware design is left to other companies, but when you make hardware without taking into account the needs of the eventual software developers, you end up with bloated hardware full of pointless excess. From the outset one must consider design from both a hardware and software perspective."
Gunpei Yoko