I agree, I like Naked more too, but some songs are definitely better on the original (like the title track). I think Phil Spector did a pretty amazing job with the original Let It Be, considering the studio tapes were such a huge mess when he got a hold of them. But a lot of songs (Two of Us, Across the Universe, etc.) were way better once McCartney took off the overproduction of Spector.
They were breaking up while making Let It Be, and they knew it, so afterwards they went in the studio and took the last few songs they had and put all their bullshit aside and made Abbey Road. They didn't even bother completely the partial songs they had, so they just made them all into one, big 16 minute medley, and made it the B-side to the album. What a great way to end the greatest rock band of all time.