Just to tackle the elephant in the room here, I recently read Secret Origins. I've owned Birthright for years, but I got SO from the library, and I'm glad that I did. It's not that it wasn't enjoyable (much more than, say, Earth One), it's just repetititve in light of Birthright. Both books share a very similar structure and hit all the key notes for Superman's origin story (both are essentially riffing on the broad strokes of Superman: The Motion Picture). The latter, however, is too beholden to the Donner films and the Silver Age to say anything new.
For instance, once Clark arrives in Metropolis in Secret Origins we hardly get any insight into his thought process. In Birthright, we're with him every step of the way as he develops the persona and tweaks it along the way. SO's Clark is already a complete character, and his Superman is too; he just has to prove he's authentic to the people. There's no learning curve, and really after the post-teen years no story arc. The Kents in Birthright are not just younger but far more provocative, with Martha having an interest in UFOs and Jonathan dealing with anger issues and jealousy/inadequacy. In SO they're saints again, with Martha reduced to sewing clothes for Clark.
Birthright restored the pulpy elements of Krypton, enough to break away from Byrne's interpretation and allow Supergirl to be reintroduced, but it also was a breath of fresh air. The chapter in Africa alone is worth the price of the book. What does SO add? Essentially the Legion of Superheroes and Superboy (and Krypto, ugh, in a completely pointless scene), and Superboy is only retconned back in so he can wear his costume in the future with the Legion because he's never seen in it until he's an adult. Johns also lends Lois Lane a strong voice, but she comes across as younger than I'd like, and brattier; certainly younger and brattier than the woman that Waid wrote.
Pointless. I guess what I'm saying is that Birthright is a superior story, and SO could have been written to accompany it rather than replace it (kind of like how For All Seasons was a companion piece to Man of Steel). In the end, however, continuity be damned as I'd rather read a good story than care about the exact circumstances of how Clark Kent met Jimmy Olsen.
In the end, they're both imaginary stories...but aren't they all?