As someone has already said, it does seem unfair to compare Pet Sounds with Sgt Pepper, since Pepper was recorded a whole year later.
Pet Sounds was being recorded around the same time as the Beatles were working on Revolver, so it would make more sense to compare Pet Sounds with Revolver and Sgt Pepper with Smile.
Anyway, if I was being sent to a desert island and could only take one album with me - either Pet Sounds or Revolver - I would choose Revolver.
But if the choice was between Pet Sounds and Pepper then I'd go for Pet Sounds.
I think both the Beatles albums I mentioned are a bit more instantly accessible than Pet Sounds. Most of the songs on Revolver or Pepper stand up really well on their own - you could hear any of the songs from those albums on the radio and most of them wouldn't sound out of place. Maybe only Tomorrow Never Knows, A Day In The Life and Within You Without You are a bit too "weird" for the radio or to be released as singles.
On the other hand, the magic of Pet Sounds comes from repeated listening, and also from hearing the album in its entirety. There is so much going on in the instrumentation, the harmonies, the lyrics, the arrangements, etc - it is impossible to take it all in on your first listen. Pet Sounds for me improves every time I hear it!! And apart from Wouldn't It Be Nice, Sloop John B, and perhaps God Only Knows, the Pet Sounds songs wouldn't come across so well if you heard them separately on the radio. I think most of them work much better when listened to as an album.
I think what I'm trying to say is that you have to work a little to appreciate Pet Sounds, whereas The Beatles are much more immediate.
I hope that all makes sense.
It's all down to individual taste at the end of the day, but it's interesting to see other people's opinions on some of rock music's greatest ever albums.