The subject line of this thread is essentially confused.
It asks the developers to stop making bad changes - but pretty much by definition, if the developers are making the changes, they're unlikely to think they're bad changes.
There's a pretty easy litmus test. "Can this mechanic be justified on a gameplay basis within the framework of the game's level of abstraction, and can it be implemented reasonably within time/budget/development/practical constraints?"
Two obvious examples of absurd tweaks are the primitive ship building (which causes Wiz to question his own credibility, or claim that primitives were overperforming and needed nerfing, take your pick because it must be one of the two) and same-continent colonization (a case of deliberately nerfing disadvantaged positions for the sake of it and saying as much). When pressed for what these add to the gameplay at EU IV's level of abstraction, the developers can give us nothing at all. The same goes for the idea group restriction, a few of the horde nerfs, and quite a few more mechanics I can list if anybody involved in decision making is willing to take this thread seriously, and the truce timer which failed to do its stated intended purpose outright. Military access is an amazing example too, it went from straightforward, but unrealistic, to convoluted beyond rationality and equally unrealistic, to no purpose and with several bugs.
This should come off as odd, even to the developers, because a large number of their mechanics they have managed to justify easily to the point where even heavy scrutiny can't overcome it. Isn't that a red flag? Doesn't it strike anyone as odd that PI can easily and soundly defend the majority of its mechanics, but then falls to utter silence or stating wrong things outright on a few of them, and can't even go so far as to explain the rationale on obtrusive changes that, too often, have been the source of some of the game's larger bugs?
I agreed with the OP in spirit, but not in its construct. Wiz's answer to it, however, tells a lot about what's wrong here. Too often, these changes aren't holding up under scrutiny or even doing what it's claimed they do.