i... i think i might have it...
At the end of the film, Teddy tells Leonard a story about helping him track down multiple 'John G.s', along with alot of other assumedly BS about lying to himself to keep him self going. I don't think it's BS, I think it's all absolutely true.
Lenny talks about ALWAYS trusting his instinct, especially in the context of Teddy... AND Natalie. Teddy WAS lying, if you believe his story at the end, just not in the way the rest of the film leads you to believe, and he was wrong about Natalie.
How would Lenny know how Sammy's wife died? Because it was HIS wife, and he only has a vague recollection of it, from her constant conditioning of him, just a very deep memory that he couldn't fully grasp.
Sure, it's all just speculation, but there's just one little clue that clinches it for me, fully and completely.
I was looking through the 'Goofs' section on this site, and there is one there mentioning the head x-ray seen in the scene where Sammy is seeing a doctor, mentioning that his condition is purely mental, not physical. The x-ray shows massive trauma to the left side of the brain. Massive trauma is physical, not mental. So if the x-ray isn't Sammy's, then whose is it? Who, in the film, has short term memory loss, and suffered massive trauma to the LEFT side of the head?
Sammy WAS lying, and the rest of his story was what happened to Lenny. His wife survived, and couldn't handle what happened, and eventually caused Teddy to give her an overdose on insulin. The reason he 'forgot' that part, but 'remembers' Sammy's story is EXACTLY what Teddy said. He needed a reason to go on, always needed a John G. to hunt down, so he removed all conclusive evidence from his research, to keep himself investigating (such as the missing pages), and got the 'Remember Sammy Jankin' tattoo, to constantly condition his own story onto someone else, effectively loosening up all the tied ends.
So, Teddy was never the bad guy, and everything he said at the end was true. He even tried to get him away from Natalie, and everything he said about her, such as her being tied up in drugs, and giving Lenny false leads, turned out to be all true.
So, yeah, there are more points, but I think if you rewatch it with my theory in mind, you'll pick them up.
Also, to be clear, I actually have done NO research, so I don't know if the x-ray has been picked up as more than a 'goof', but for me, it seals the deal.