-Anakin as a mostly unlikable character;
-Anakin and Padmè’s relationship developing so fast, was hardly believable;
-Anakin’s decision to quit his duty to save her mother. I understand what was GL up to with this, but does Anakin actually have to endanger Padmè too?
-Jango Fett as the genetic source for the Clone Army;
-The Arena. Though I admit the first part (before the jedi arrive) was well directed, I just found the whole concept a bit out of place, somehow forced;
-The DS’s plans already completed more than 20 years before its construction;

Objectively, it wasn’t the worst film ever: the plot was overall well designed, directing and compositions were fine too. The real problems were dialogues and acting, and this is really unfortunate (thankfully, foreign dubbings were able to fix this). Then there’s the editing which was… functional, sure, but could’ve used more craft, especially in using the score, so to make the scenes more involving.
As a SW movie, having even more characters somehow related to each other, was unnecessary and, personally, partially ruined my experience. The same can be said on the increasing use of bad CGIs, the addition of more goofy characters (especially for villains), most of which seem out of place in SW even after ROTJ.