For controllers, camera inversion is the biggest one for me. Pulling back on the stick needs to make the camera look up. Every game should have this as an accessibility option, since it's a make-or-break thing due to how individuals can be wired.
Other than that, making shooters similar is a major thing for me. The right-stick-to-melee works really well - I got used to it because of Borderlands, and due to the excessive amount of that I played, I had to swap things like Destiny to it as well. It works out nicely - especially with an Elite controller, so the face buttons can sit nicely on the paddles, effectively allowing me access to everything that isn't the D-pad while also not taking either thumb off of the sticks.
That aside, there's some commonalities I like to establish in things like 2D action games, for example - having a dash or backdash not be on L/LB/L1 feels awkward and wrong. Super Metroid is another great example of a control scheme that needs changing, as the default is just bizarre by all standards set at the time (and to this day, as it turns out).
For PC games being played with a keyboard for movement, I swap WASD to the obviously-superior ESDF, which often necessitates that everything else be able to be changed as well.
