One thing that really bugs me is when everything is mathematically linear or constant. Take potions in Skyrim (and many other games) for instance. A potion lasts for exactly X amount of time with full effect, and then instantly stops working. In reality, drugs/medicines tend to have an exponentially decreasing effect over time as the body eliminates the foreign compound. This makes things really “gamey” and over-simplified. I'd like to see better mathematical models used (typically operating in logarithmic/exponential space rather than a linear one).

The same thing could be said about e.g. carrying capacity in most games. Rather than a gradual reduction in movement speed with increasing carry weight, there is typically an instant change from full speed to super slow (again a problem with Skyrim). The Long Dark does a pretty good job with this, by gradually reducing speed as weight increases, though it is still stepped, rather than continuous transition.

Unbalanced sources and sinks. It is typical for money to be tight for the first half or so of the game, then be moderately available, and eventually to be swimming in money.

Long running online games will eventually have the game currency collapse and new player-driven currency develop based on what players actually value. Usually the player generated currency is about the time required to farm resources.