I didn't like the Dragonite situation that much because they could've at least used him to take a fresher approach to reasons why Pokemon are disobedient. Plus, I didn't really like how he was an unusually aggressive Dragonite either. It went against my long-standing ideas of how Dragonite are sweet and helpful until angered. Plus, it kinda reminded me of Ash's Charizard, and I thought Charizard was just an ungrateful, arrogant jerk until he started obeying.
But getting back to Dragonite, I know not being sweet and innocent by default helps him stand out, but he's still a Dragonite, after all. It would've worked better if we didn't already spend over a decade with the idea of most Dragonite being kind by default.... Plus, I think a Dragonite's face just lends itself better to kind/neutral expressions IMO. The artists did a better job of drawing aggressive Dragonite faces in Johto and the Orange League. But the differences in how they draw the eyes/face make Dragonite's angry faces look uglier now.
My proposed change is that they could've had Dragonite be more of a politely patronizing Pokemon. He's sweet to her, but then disobeys because he thinks he's doing Iris a favor by making the "right" decisions for her and letting her take it easy. When she disapproves, then he just shrugs her off and thinks she's just being a cute, silly little human. Making him obedient would still be hard, because he would have to realize that his "helpfulness" is actually hurting Iris.