I think some of the issues origin from the way Commodore layouted and named the control ports.
Control port #1 is the one farthest from the power button and is mapped in memory at 56321. However its pins are combined with keyboard input, which can make it harder to use.
Control port #2 is the one closest to the power button and is mapped in memory at 56320. It is mostly free of conflicts with other input and thus easier to use.
Some game publishers may have thought it made sense that port #1 is the one to use primarily, despite it is harder to program for. OTher publishers may have not bothered, and preferred less issues so their games were primarily controlled through port #2.
If Commodore simply have labeled the ports on the outside so the one closest to the power button was #1, or even rerouted the circuit board (or changed the inputs of the CIA 6526 chip), they could have had port #1 to be free of conflicts and probably more standardized to use.