Persona 3 had too many cliches (Yukari the typical high school girl, Junpei the pervy comedy relief, Mitsuru the perfectionist). The story was cliche as well. At least in Persona 4 the characters felt a bit less cliche, and thus more relatable.
I'll take the cliché characters of 3 over the insanely over the top anime characters of 4 every time. Them cast of 3 being so grounded made them far more relate able than 4 (to me at least.) "I'm a guy struggling with sexuality but there's this boy I like but oh wait it turns out he's a girl pretending to be a boy!" & "I'm a magical teddy bear that turns into the most beautiful Arian boy you'll ever see!" never quite gelled with me personally. To be fair, I'm generalising the character's whole motives but no more so than you with the examples you gave.
Also while Persona 3 had some good social links, it suffered from some incredibly basic, boring ones as well (such as the Bookstore)
Woah. The bookstore couple was a no nonsense story of dealing the loss of your child. It wasn't the flashiest but it had one of the better moral tales to it.