I've been on a game conference this year and this topic was largely discussed and spread around the community. We don't need to read much on infinity forums to notice the trend there.
Probably the biggest single source of bad rule and mechanics decisions comes from the fact that most game designers, rather than actually going to a library, base most of their research on the work of other game designers. In this way errors are compounded, unrealistic ideas are perpetuated, and design flaws from the earliest of games become commonplace in all modern iterations.
At this stage, this is where all the trouble begins.
The two biggies are:
* The focus on combat as the core activity in games that are purportedly about assuming a role.
* Arbitrary and unrealistic characteristics ascribed to weapons and armor, very convenient for calculating casualties in mass combat quickly yet wholly inappropriate for small-scale tactical simulations
It is difficult to underestimate the ability of people to consider themselves an authority on things when their only source of information is a game manual someone else wrote before them, which was in turn based on another game manual, etc. etc. Things become worse when these designer-types elect to "make a few little adjustments" in the thirdhand systems they're stealing from.
Infinity is full of it. One thing that should keep popping up there throughout long and rambling dicussons is the idea that "This thing doesn't work unless these other things also work." This interrelationship of elements in a system can be considered "holistic," and is a good thing to keep in mind when designing, tweaking, or patching a system. Everything affects everything else.
Somehow, established professionals in the game development field forget this idea all the time, or perhaps never considered it. As a direct result of thinking about game design in a non-holistic way, elements are introduced into the game for seemingly decent purposes and wind up destroying whole areas they were never meant to impact. However, because designers of all types tend to be stubborn, proud people, these mistakes are often left there to fester, and the game is never quite as good as it intended to be.
The spread of ideas and correlations in infinity is disturbing to see at the moment.