I think for me it’s Let It Be. I thought the “Naked” version was better for the longest time, but a few years back listening to the original album made me really love it. I think the ballads and slower songs are still better on the Naked version, but the rest sound so full and energetic on the original.
For a long time the naked version of “I Me Mine” was my favorite underrated Beatles song.
I Me Mine is such a good song, and the Naked and original versions are both great!!