The biggest mistake by Lucas was making 2 different Anakins because of the age jump. He is the reason we are watching these three movies, and when you want us to follow a boy in TPM, knowing that there will be a new actor to play Anakin for the next two, it is hard to invest your likings in him.
So for years fans wanted to know who Darth Vader as a human really was, and now you were asking us to like or love two different actors? To me any actor that is cast is always hit or miss, sometimes they can be dead on with the public, sometimes they revolt cause it is a bad choice.
I never truly cared for Anakin and Padme through the PT, and if the viewer can't care, you won't feel the tragedy that bestows them in ROTS. Now for fans that cared for them, ROTS is a powerful movie for them, but so many fans I know didn't either love or like the two main leads for many reasons.
We didn't get 3 movies of them. Because of Anakins age with starting the PT, the grownup Anakin that turns to Vader is only seen in 2 movies, and to me you lose that trilogy characters arc. Sometimes it takes one movie just to get to know the actor, and then the second they can establish themselves and find their footing, and the third movie really shine.
To me Hayden, although Lucas intentionally wanted it this way, was whiny and in the end unlikable in AOTC. I think he was much better in ROTS, but in some ways it was too late. If we had 3 movies of Hayden, the backlash of AOTC, and his unlikability wouldn't have been as bad.
Another failing for me personaly was the chemistry between the characters and mostly Hayden/Natalie. The romance just came across as forced, and again I go back to throwing it all into AOTC, instead of really developing it in TPM, and then let it drive the story for AOTC & ROTS.
To me either you have chemistry in movies or you don't, there isn't a button that clicks on when you yell action. Though I don't love Titanic, DiCaprio & Winslet had great chemistry, Cruise & Zellwegger had great chemistry in Jerry Maguire, and Crystal & Meg Ryan had great chemistry in When Harry Met Sally. There is no formula, you just put the two leads together and cross your fingers.
So, my biggest failing and why Lucas failed for me is at the end of ROTS, I should have been more emotional when the characters we followed for 3 movies all went south. Mace flew out of a window, ahh, I didn't really care, but he is still great in Pulp Fiction. The jedi were getting extinguished in Order 66, which was actually done well in the montage, but did I really know any of those jedi except the conehead guy? Padme loses the will to live? Wasn't she this strong willed women who just gave birth? And finally Anakin laying there legless burning up, I should have been in tears, and I was like thank god, put him out of his misery Kenobi! Kenobi was the only who really tugged at me at the end when he was yelling at Anakin, "You were my brother, Anakin." "You were the chosen one!" That gave me goosebumps, because Kenobi was the one true character you follow for three movies, and there no contradictory character hicups like that senator who lost the will to live. Kenobi was the one real character to me in the PT.
So again, I am not criticizing anyone for getting emotional in ROTS, to each his own, but for me Lucas failed cause there were some heavy moments at the end of ROTS that should have moved me, and unfortunately they didn't.
That to me is the biggest failure of the PT, in the end it is always about the characters.