Lets see ones off the top of my head that ive played are:
Pokemon Glazed (great story extremely long difficult level medium to hard up to 6th gen pokemon some Megas all legendaries continous plot changes custom sprites)
Pokemon Ruby Destiny Series (theres several games in the series which have a great storyline are super hard but lack custom sprites and im pretty sure they dont have 6th gen pokemon)
Pokemon Victory fire and pokemon resolute set in many different regions custom sprites 6th gen pokemon great storyline really no complaints long game pretty hard grammar isnt great but both are completed resolute is sequel to victory fire but you can just skip to it if you'd like :p