I think this is a good question to answer, so I'll address it with my perspective.
Step 1.
When I learn a song I break it up mentally into sections.
1. Intro
2. Verse
3. Chorus
4. Vamp/hook
When you break it up that way it's a lot easier to remember what the progressions are and you'll soon find that a lot of songs are all using the same progressions in these same areas, but just played with a little different timing.
I DO NOT learn note names when playing/learning a song with the exception of knowing what Key I'm in. The progressions take care of what notes I play, so I don't worry about it at all unless we change stuff up on the fly and even then I translate that to a progression and forget about what notes I'm playing. Now if I think about it I can tell you what I'm playing, but I'm more focused on playing music than knowing exactly what note I'm playing.
I don't think that ANY of us should be learning songs to the T! If you're worried about learning a song lick by lick then you are seriously hindering your growth as a musician IMHO. Now you might be asking why, so here's a few reasons.
1. Even the people that played the original version aren't going to play it exactly the same way after they cut the record. It's just not going to happen. There will be similiar concepts, but rarely if at all will you hear someone play their own song the same way twice.
2. Why learn it to the T and it's more than likely never going to be sang exactly how the record is? We all have been there when things vamp out, or they repeat a verse, or whatever and one of two things happens. A) we repeat exactly what we did on the last verse and it becomes a carbon copy (I HAVE BEEN THERE AND NEVER WANT TO GO BACK) B) We ignore our natural musical voice and become a copy of someone else rather then being your own "musician".
Now with the 2 points above I'm not saying that we shouldn't study licks that others have done or try to figure them out, because that helps us learn and move around our instruments, but when it gets to the point that all you can do is mimic what you hear and you can't apply any of your own personality to the music, you've become someone that isn't someone.
Step 2.
I apply a groove/feel to it and this steadily evolves as I get more and more comfortable with the feel and how the other musicians are approaching it.
Don't feel that you have to have the feel right off bat. It's not going to happen for most of us (especially when you're hearing it for the first time).
based on ur explanation, i find it quite reasonable to conclude that, for the most part, we are NOT learning the same songs, which is a large reason for the discrepancy. either that or your skill level is far beyond mine.
I been doing this method u described for years now, probably since i started playing (i have that engineers mind so i tend to break down everything in like manner) and im pretty good at it. in fact some songs i can learn on the spot and there are some i can get the basics of in like 5 minutes and take the rest of the time to perfect.
but i do come across songs with many and/or weirdly timed breaks and movements. those are difficult to get down. its one thing to say "there are some breaks in this song" as opposed to being able to do them (i think thats one thing that add to the time of me learning a song)
also i somehow keep coming across songs with seemingly excessive (well i think its excessive) non-diatonic chords as prominent parts of the progression (not passing chords). that makes it insane for me to figure out the key and determine the pattern. if you have a b2, a b5, and a b6 chord you actually start to think its a 1,4,5 progression in the key a half step higher...until u run into chords that suggest thats not the key. some of the well known tricks work and some dont.
I read a theory book that says you can use chords from both the minor and major scale intertwined because they both resolve to the same root. For instance you can use both diatonic chords from Cmajor and diatonic chords from Cminor together because they both have C as a tonal center. Explored it on keys and its sound and actually identified some stuff that i couldnt figure out in these songs, so i think thats partly whats being done. Its still hard to catch by ear sometimes.
but those traditional same ol' choir songs. yeah, i usually catch those easily as well as the simple p&w songs.