My ds2 was exactly the same as your son in that he was very popular in his old school but completely the opposite at his new school. he is very intelligent, so sometimes a bit serious for them, does not like kids mucking about, has no interest in football and is also quite immature for his age (well, not how I would describe it, necessarily, just not old before his years).
Anyway, he is now in Yr 4 and seems a lot happier. It helps that he has a brother in Year 6 who is immature and they seem to have mutual friends in Yrs 4,5 and 6, but what I think has really helped ds2 is developing an interest in something "cool" even though it isn't the ubiquitous football. Anyway, he has a gameboy and likes Pokemon and suddenly he has found other boys who play computer games and like Pokemon.
I think your son has to find himself an interest - no matter what - and then hopefully he will find someone else who shares it. Have you any idea of anything that would appeal to him that would also appeal to other boys?