The biggest mistake the Beatles made was not putting Penny Lane/Strawberry Fields on St Pepper. It is already a great album, but with those two on it, man, one of the best ever from anyone. My only complaint about St Peppers is the guitars are faint in some of tracks. There is great guitar work on the album for sure, I just wished they would have pushed them more forward in the mix. For example, this was noticeable to me when I saw Rain, a Beatles tribute band, play Lucy In The Sky With Diamonds. In the live setting, George's psychedelic guitar that fades in and out in the song sounded awesome, really added to the song. In the album mix, you hear it, but it is not as prominant. Check it out here where it is isolated (3:36)
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But, I am nit picking of course.
I like your analysis. I don't think I've considered the guitar mix w/ Pepper, I might rabbit-hole that at some point.
Similar to Penny Lane/Strawberry Fields not being on SPLHCB, similar could be said how Paperback Writer/Rain on Revolver would have been apt and I would have no problem swapping those for a couple that are on the actual LP.
But those choices were typical of the time ... when pop music was singles-oriented and AOR hadn't "arrived," so it made $ sense to release 45s that weren't part of an album.
That's my Rambling Cliff Notes version of the situation. Many other CF music fanatics including @MeanDean can summarize better than I did.