hopeful's final fight against hart in the beltboy route had benny be assisted by the visions or spirits of liam and clyde, though it's implementation is a bit flawed because hart could attack them somehow

sowts, for example, did something fun with enemies who use fire, you could extinguish their flames with the +wet status effect

infinity unfolds had a cool mechanic with the hugo fights where you needed to parry his attacks with the right input timing, or mash to get out of a grapple in the infinity route

brad has a pain had this one enemy who tries to add you to his inventory which instantly nets you a game over, he changes his sprite every turn through a custom script

buzzo revamp had a mechanic where buddy's head just explodes if you get her hp to 0 or you take too long to beat buzzo, effectively punishing the player for using aoe attacks

aaa's mod where you play as brad chasing fardy also had a lot of fantastic scripting in it that made it function, the phrase "fantastic scripting" can be applied to most if not all of his mods

then there's all the mods where the enemies have combo dial attacks and even timed attacks where you have to press a button at the right time to nullify them

or all the mods where they used scripts to have more than eight enemies in a single fight

the few enemies in bashful who had multiple phases could have said phases easily skipped with the cocaine cheese strat because said enemies don't heal after entering their next phase, the warden is probably the most disappointing one considering he's supposed to be a major fight

bashful also had a missed opportunity to lean in even harder on the jojo reference with the not-jotaro being a blue mage who could copy the attacks of party members, it's tedious but still surprisingly simple to implement