Would it not be a universal issue if it was the game?
Indeed, and no other application or game on my system is like this. I can play BF4 at maximum settings at 60fps, same with Star Citizen etc.
Of course, what you're trying to say is that other people should be experiencing this.
This is genuinely the first I've heard of glaring Minecraft performance issues and I know of many people who run it at 60fps or more on far lower spec systems than you're running.
This is no doubt in my mind because people who struggle with this just give up on the game and don't bother. So they aren't participating in your community. I have only met two other people who had this issue too, but considering that I only know 12 people who have tried/played/play Minecraft, that's not really unsurprising. I do know that the issue is definitely exasperated when bumping up quality settings and fullscreen.
There must be something that Minecraft or Java/JNI doesn't like about your specific hardware configuration, but I really couldn't guess what.
I honestly think the game was written poorly. I remember a time when overflows (corrupts your map because you went too far) could happen because you went too far and it was because Notch did not use a feature of Java that used to be advertised as a big reason to use Java... Bignums. Then instead of actually fixing it with bignums, he just hard codes a barrier. Instead of using literals to represent all the data in a grid, he chose to create some of the most inefficient way to store that data and we end up with servers that require 12GB for a modest Minecraft server setup. He could have created zoning with bignums, which would have allowed only the relevant portions at the time to be loaded into memory.
I am convinced based off what I have observed from decompiled Minecraft classes and the solutions that were chosen to solve problems that the issues I am experiencing are from a poorly designed and poorly implemented engine that causing some issues with my system.