Thanks, I was afraid I screwed up with my very first post here. Sort of like showing up at a party where you don't know anyone and right away spilling a drink on the host.
Anyway, just because I like stuff like this, I'm going to propose a new theory. (And no, I don't seriously believe this either. I'm just doing it to show how "clues" can be interpreted many ways.) Here we go:
Ringo is dead!
That's right, the clues were real, but we got the wrong guy. What if it was Ringo who died in that car accident, not Paul? Let's see...
Sergeant Pepper: Yes, the cover is a grave site, but if you look at the wax figures of the "old" Beatles, Ringo is in front of the other three, not in line. He certainly looks the saddest of the four, and Paul seems to have his hand on Ringo's shoulder, comforting him. In the actual music, when the band sings, "So let me introduce to you the one and only Billy Shears," who then starts to sing? Right, it's Ringo. If they meant that Paul was Billy Shears, they would have gone into Fixing a Hole, not With a Little Help from My Friends. And don't forget, a couple years later, in I'm the Greatest, Ringo sings explicitly, "Yes, my name is Billy Shears. You know it has been for so many years." Surely a confession. Speaking of With a Little Help from My Friends, Ringo is the one who asks, "What would you do if I sang out of tune?" Is he worried that he won't fit in as the new Ringo? But no, he "gets by with a little help from my friends." The other three are helping him with his impersonation. All of the other lyric clues on Sgt. Pepper still stand: "He blew his mind out in a car", etc.
The White Album: It's Ringo who sings, "you were in a car crash, and you lost your hair." Was he singing this to the "real" Ringo, the man he replaced?
Abbey Road: Yes, the cover is a funeral procession, but at least in America (I don't know the traditions in England) the body of the person to be buried usually goes before the mourners, who follow behind. Therefore, John is the minister/priest/whatever, poor Ringo is the corpse, to be buried in his best suit, Paul is a mourner (surely being barefoot must be a sign of mourning in some culture somewhere in the world) and George is still the gravedigger.
The Batman comic book, shown earlier in the thread, nearly gets it right, or was it planted to show the Beatles' real intent? In the comic, the band member who's thought to be dead, confesses at the end that he's still alive; it's the others who were killed. Maybe some of the "Paul" specific clues, like the black carnation in Magical Mystery Tour, were intended to focus our attention on the wrong guy, so we wouldn't look too closely at Faux Ringo.
The other clues about car crashes, death, three Beatles, etc. could simply be referring to the death of Ringo, not Paul. In a way, this makes more sense than a fake Paul. At least according to legend, Ringo got more fan mail than any of the others, so it would be important to keep his death a secret from the fans. And it would certainly be easier to cover up his death than Paul's; you don't need to explain how this imposter could write songs as well as a Paul imposter, or sing as well. Ringo didn't write many songs, and no one ever said he was a great singer. Likeable, but not great.
I'm sure if I went through all the albums, studied the covers and played the songs backwards with this in mind, I could find more clues, but this is just off the top of my head. I would have placed this post in the "Ringo is Dead" thread, but for some inexplicable reason that thread doesn't exist. A cover-up?