I'll throw my hat into this!(been wanting to use tht saing for a while now)
I'll admit, i'm a Sony Fanboy.....So i'm going to say GT5 is better for me!
But i'll say why, I'll admit i've not played FM3 much appert from at a mates house and i could't rember much the next day....but the game was ok overall. Ther was just somthing lacking compaired to the GT games though, and that was the cars.
Now i'm not sure the whole ammount of cars in FM3, but with the GT games they always have a huge list car everydy cars, or more comman cars! Such as the S13 silvia, MR2(AW11), Suzuki Cappuccino.....cars that wont really appeal to the 'mass car fans'(if its not on TG it's not cool sort of thing) and thats partly why i like the GT games....it also got me into JDM's alot! the game also gives the feel of a Trackday rather than a proper race!(unless its a actualy race, with LMP cars, etc)
Now i havent played FM3 properly(as stated) i did play FM2 a bit more(note, A bit) and it just diddent do it for me admittidly. Maybe it's that i'm not used to the controller, or i'm thinking it for another game. But rember this is my personal opinion!
So yes, i'll say the GT games are better, but thats as i havent really played the FM games so you could say my comparison is't really a worthy one! Although i will be playing FM3 soon as part of a GT5 Comparison for a games review site(which is't finnished yet) so i guess my opinion will be changed by then!