I don't see why you can't have an option during install that asks you whether you plan on using myPlex or if you would rather set things up on your own. You could even label them as default and advanced. SO then the user would have only one authentication method running on that user's server (and other one just wouldn't install). I've used an older version of Plex until recently and for the last few days I've been pulling my hair out trying to figure out why I'm unable to connect to my media remotely (even though my router and everything is set up right). Now I know why. Which is very unfortunate, because no offense to the Plex team (I LOVE your product), but I refuse to use myPlex. >in my opinion< I feel that it's an unnecessary security risk. Not only would the IP address to my computer be on the myPlex server, but the login as well. Which means that whoever has access to that info can get on my computer. Now I'M NOT SAYING that Plex would ever do such a thing, but I don't know them personally, so why would I give them the keys to my house? Right? Another thought is that they could get hacked in the future (which I hope they don't).
There's certainly no technical reason we can't do that. But then we'd have to continue supporting both login methods in the server code. And implement both login methods in every client. And add user interfaces for controlling both login methods to the server, and also to every client. I understand your point of view, but to be honest, you're in the minority. Most users are perfectly content with using myPlex. We're a relatively small development team, and the cost in terms of time & work for supporting the aforementioned feature in every codebase outweighs the benefit it'd provide for the handful of people who'd actually use it.
If you really don't feel comfortable using myPlex, there's another option - you can disable security entirely and handle it yourself, using a VPN or SSH tunnel.