How is the protagonist not the main character in the OT?
What is an example of a story in which the protagonist and main character are different? (I'm sure stories like that exist, I just can't think of an example right now.)
Anakin is neither main character nor protagonist in the OT. Anakin isn't even
in the OT until the very end, so that rules him out pretty conclusively. You can't be part of a story that you're not actually in.
However, this debate got me thinking - it's perfectly possible that the events of the OT could be restructured into a story where Anakin or at least Vader/Anakin, thought of as a single character, is the main character/protagonist.
That would be a different story than the OT we actually got, and would require three completely different movies to be made, but just as an interesting exercise, let's see how that would work.
First off, we need to get the guy into the story to begin with. It's still unclear exactly how much of Anakin was present in Vader. Was he completely submerged? Was part of his personality present, and if so, what part?
This all has to do with the still-fuzzy issue of exactly how much mind control the dark side exerts - the Mortis Arc depicted Ahsoka as totally controlled but Anakin only partly controlled, so maybe being the Chosen One makes him somewhat immune to its effects.
So the first job of the New OT is to establish that, yes, Anakin is still present in Vader's consciousness, and to further clarify just how much of him is in there. The New OT will have to treat Vader as more than just this really cool cipher in black armor. It will have to stick with him in scenes that give us a solid understanding of who this new character - Vader/Anakin - really is.
This is going to be tricky because he's gotta do a lot more than stomp around, shake his fist and force-choke people. He's got to have dialogue that clues us into who exactly is under that body armor, and it makes no sense that he'd be spilling his guts to the Emperor or some hapless Stormtrooper, so I guess he's going to have to spend a lot of time talking to himself.

Maybe there can be scenes that delve into his consciousness while he's meditating. Maybe his mind travels to Mortis or some such. Anyway, that's a creative problem that can be solved somehow.
For purposes of discussion, I'm happy to regard Vader/Anakin as simply an iteration of Anakin, rather than a completely new character. However, we're talking about TCW's Anakin, not the PT Anakin, because there's simply no way to graft a whiny little bitch onto Vader's character and have anything coherent as a result.
After that, we need to see the events of the OT from Vader/Anakin's perspective. That might involve events that are completely new. What was relevant from Luke/Leia/Han's perspective won't necessarily be the same as what's relevant for Vader/Anakin's story.
This could be a very good story, and would make a good animated series - to finally tell us what was really going on under all that body armor. I don't see why we can't have a parallel story of the further adventures of Luke/Leia/Han. One series could alternate between perspectives perfectly well, just as TCW alternates between the stories of several characters.