And this is a huge but. He was unable to achieve for me to care about the characters from the PT anywhere near I did from the OT. So when I watch the PT and all their fates, mostly Anakin paralleled to Lukes is lining up by ROTS, I could care less what happens to him. He makes Anakin so unlikable in AOTC, by the time he is burning in ROTS, I was hoping Kenobi would put him out of his misery. He should have made Anakin AS likable as Luke, but he was a more flawed man than his son, that to me parallels more than taking the easy way out and just making him pout and moan for 2 hours.
Second, he was unable to connect the trilogies visually either. You have one huge CG trilogy filmed in front of bluescreen, with the exception of Tatooine in TPM, which usually looks like one big animated movie with real actors. In the PT, the planets are exotic, and all swooping overhead shots to introduce us to this world.
Then you have the OT where 90% of it was shot on sets or real-life locations where you actually feel like the actors are in the world. Tatooine is shot in Tunisia, Hoth is shot in Switzerland, and Endor is shot in California. The models in the space battles, while may not move as fast or fluidly as CG, look realistic and don't look like one big video game like ROTS space battle does with EVERYTHING going on in the screen.
The third problem is the scope of the story in each trilogy. The OT is about the macro part of SW that centers around these characters, SW '77 is about rebels vs empire, not about Darth Vader vs his kids. The trilogy moves more personal about father/son but never loses that sense of the rebels vs empire as they all celebrate on Endor.
The PT is about Anakin with the macro stuff littered through it. Unfortunately Lucas chose to make this story soley on Anakin, and key things that would marry the trilogies: Expansion of the Clone Wars (Watch the Cartoons), The force Ghost Trick with QuiGon (Read the Book), Padme & Bail creating the rebellion (Watch ROTS deleted scenes) are thrown by the waste side for Anakins story.
So for lovers of the OT, they feel there is too much Anakin in the PT, and it is tough for them to marry the trilogies for that reasons. For lovers of the PT, they feel the OT, and mostly ANH, does not have enough internal Vader, and find that the parts of Luke, Leia, and Han scenes, especially the rescue in Jabbas Palace, tedious because they see it as the story of Vader, not these rebels.
For me they will always be two trilogies, and if Lucas was able to have one linear story, of either Darth Vaders biography, which is thrown out the window by Episode IV, or the story of how a society goes from a democracy to tyranny and back to a democracy is thrown out the window the minute a 10 year old Anakin is placed in Episode I, and totally throws off the whole balance of the OT.