For me, I lean toward NAKED but a lot depends on individual songs..
Regarding Long and Winding Road, I tend to enjoy the string arrangement better -- but you have to consider that this is the version I've lived with for 34 years! It doesn't sound the same without those strings. Having said that, I also enjoy the NAKED version too. They're both different and enjoyable.
As for Let it Be I like the version on the original LIB album the best, hands down. The guitar solo is great. I agree with Frighty on all he said about this one. Never liked the single version (PAST MASTERS 2) as much.
I'm most happy about Don't Let Me Down being included on NAKED at last -- and I love the version they used.
I've Got a Feeling is my favorite track on NAKED -- I think it's much more rockin' and I prefer it to the original version.
Get Back sounds better and clearer on NAKED, and I actually could hear more of Paul's intonations and slang on the words ("for some Californiaor grass"). But I miss the ending with the "passed audition" and - even better - the single version with the climax and fadeout.