It needs to be said over and over again. Complaining on a forum isn't going to do anything. Pissed off by this, upset by this, etc then actually provide actual feedback. This is one of the rare times where there is a direct way to do so to Nintendo. Use it. Remind people of this over and over again because there a lot of people that love to just complain and won't actually take the next extra step to get those complaints to the people that need to hear/read them. You see it in politics all the time to give an example. People that will bitch and moan about something but can't be bothered to pick up the phone and call their representative in the state government or congress and leave a message. Some won't even bother with the websites that will send a letter automatically where the only thing you need to do is fill in your name and added an email address. People that will not bother to put in the time to education people to vote one way or another in regard to something they dislike. Not even a family member. Reminding people that there is a way to directly give feedback is the very least one can do here to get Nintendo to understand what the damn problems are.
You got it! Let them know with every avenue available to you. Their email, Facebook, Twitter, the in-app suggestion box, through editorials/articles on websites, etc. They've changed things before based on feedback.
It's also not like they couldn't find a solution to this soon enough. There are USB ports available for setting up a dedicated Bluetooth "line" for a headset solution (or something, I don't know) that wouldn't interfere with the controller's Bluetooth connection. Then they could move some of the functions to the console, leaving the phone for extraneous things (see what your friends are up to, leave messages for them, etc., and who knows what other things they want to do with the app down the road, such as setting up hotspots or whatever) and another option incase you don't want the "Pro Headset" attachment for the dock.
But, why would they bother if enough people don't get onto them directly about it?
Also, that literal wire squid is a sight to behold!