Why does switching spaces change the focus

I have opened a bug, 22959637, but it has been several months, and I am not sure how to get it pushed up the chain. So, I figured I'd toss it out here and see if anyone else has a solution to this (that I have missed) or knows of a way to get apple to look at it.

If I created several "spaces" or desktops or whatever you'd like to call them, and switch between 1 space and another, and then back to the 1st, often times the focus of the active application has changed. There does not seem to be any rhyme or reason to it. As an example, if I have Eclipse open, it always comes back as the in-focus app. However, even within the Apple products, iMessage, Mail, Safari, the focus can change.

How hard would it be to have a setting (or, is there one) that simply states, leave the focus of the apps in the space unchanged when switching from one space to another (and back).

I am currently using El Capitan, but this happened with Yosemite and prior versions as well

Any thoughts?