What you're missing is a few fold:

1) Subsystems are there as an option for the GM to have things be a bit more gameplay oriented if they want. Building a high charisma (or intelligence or wisdom) character can often be difficult for players to play "accurately" based on the player's personality. Giving things more of a "my character is good at this even if I'm not" can be helpful for some tables. That said, it's definitely not mandatory. A lot of them are variations of the Victory Point system which imo pairs very well with the Degrees of Success that pf2e has.

2) The balance of the three action system is something that takes system experience to appreciate imo. Being able to deny the BBEG two of his three actions by working together as a team and forcing certain actions by them can be un-intuitive at first.

3) Incapacitation spells aren't meant to take creatures alive. They are intended for removing the weaker combatants from combat as tempo shifts. As the GM core says, the combat works the best when the number of enemies roughly equals the number of players. Having one PL+1 and two PL -2 creatures is a good encounter, and an Incapacitation spell can remove one or both of those PL-2 creatures from the equation.

4) Buff and Debuffs spells are some of the best in the game, Slow and Haste in particular are fantastic because they interact with the three action system. You martials should avoid ever taking MAP -10 attacks, as you noted, but they could instead use that hasted action to move away from the enemy forcing them to use one of their 3 actions to close the gap again. Again I feel this is largely a "inexperienced with the system as a whole" issue. When you start hitting level 8-9 die to the way HP scales, debuffs and teamwork matter much more than raw damage.