None of those are included by default, but since this is just a Game Maker project it wouldn't be impossible to include them.
- More than 4 moves per monster would be relatively easy, just add a few more fields in the monster data structure and increase MONSTER_MAX_NUMBER_OF_MOVES accordingly. The biggest effort here would be to resize menus so more moves will fit visually.
- Item to teach a monster a new move would be a bit more work (needing some custom menus) but ultimately you should be able to leverage the existing code for learning a move by levelling up here. You probably want some data structure for which monster can learn which moves, too (a big reason I didn't include this was because I figured it was too much work setting up a system like that which would still work for every user's use-cases).
- Passive skills would need to be added to the monster species data, but ultimately would be similar to held items (check obj_battlecontrol's step event and look for all calls to the function "battle_item_might_affect_this" - you'd basically do the same type of checks, but for passive abilities). I.e., the skill has a trigger condition like "on damage" or "after your turn", and you check if the affect monster's passive skill has that trigger; if so, you invoke its effect script. (And then the script decides if anything happens - an ability like Flash Fire or Spiky Body only triggers its effect on certain types of moves but you would run the script every time the monster takes damage anyway and let it decide based on current attack data and such)