There seems to be a lot of polarization of preference regarding the "two Sonnys". IMHO, the main difference is most notably in his sound- it really changed. I'm sure Sangrey can and will detail this.
As for my preference, I can't choose- I love the Vanguard sessions, that's some of my favorite Rollins. Colossus, Newk's Time, Volumes 1 and 2. He has really assimilated the bebop language on the late 50s stuff. I'm guessing the "average listener" might consider the 50s stuff to be generally more "accessible" than the 60s stuff.
To me, the 60s Sonny has a lot more of the "outness" associated with the avant- garde music of that period combined with his staggering harmonic vocabulary. There seems to be more spontaneous variation in his sound (sort of "phasing") in this period. The RCA sessions are amazing- the long version of 52nd Street Theme is a rhythm changes clinic. Now's the Time w/Herbie is great. If Ever I Would Leave You w/JIm Hall is great. The stuff w/Don Cherry is great. Etc., etc., etc.
He, more than any other player, makes me laugh when I listen to him- due to his astonishing imagination, vocabulary and execution as well as his extroverted sense of humor. The Coleman Hawkins session always cracks me up.
Count me as a big fan of all Sonny.