"Naked" is far superior sound wise, because it's been remixed. It leaves out novelty tunes "Dig It" and "Maggie Mae", but adds the brilliant "Don't Let Me Down" (which was the b side to "Get Back").
Certain bits have been added or left out from the songs, I'll get into this later. When I'm posting my review, hopefully sometime next year.
Personally, if you disregard that "Naked" has remixed sound, I mostly prefer the original album. With the possible exeption of "The Long And Winding Road". But both version has their charm. The original version has Spector's lush orchestration, but some of it really adds to the song. The "Naked" one has a beautiful organ solo by Billy Preston. "Across The Universe" is the other one that's radically different. The original featured Phil Spector's orchestration, "Naked" features a, well, naked version of the song. My fave is neither, I prefer the "Wildlife" version, which can be found on "Past Masters vol 2", which feats some lovely backing vocals among other things.