I agree with you in regards to the main cast--although, I would also argue that the "using people" feel from P3 may have been intentional, considering your group is, essentially, a student-run covert ops group, funded by a powerful military contractor (or else just a mad science corporation). The clinical relationships, especially at the beginning of the game, feel very appropriate with the theme/mood.
P4 has great inter-party S-links, but I found the other ones--your fellow students--so less...impactful. Most of them were kind of selfish pricks, or else their "huge problem" was relatively minor. I mean, in P3, you get your heartstrings tugged by a little girl desperately trying to stop her parents from divorcing! You get a gender-confused foreigner who is desperate to fit into and stay in his adoptive homeland, you have a star athelete forced to abandon his dream and college in order to fulfill familiar obligations, you had a miserable old Monk who has been left by everyone he once loved, and all of these characters are really touching and tragic.
In P4, you still have some like that (the estranged mother comes to mind, as well as Yukiko and Naoto) but a lot of them are far less...heavy, I guess? I mean, you have one kid who can't talk to girls, one girl who just selfishly hates her father (I can understand from her circumstances, maybe, but she REALLY treats him like dirt and she doesn't explain herself well), you have some high school primma donna, and you have a sexy nurse who acts like she has a deep dark secret, but really doesn't.
I'm not saying they are better or worse. But even the silly S-links of P3 resonated with me. A lot of P4's S-links it took awhile for me to even warm up to the characters, and solving/advancing their personal problems didn't have as much an impact on me.
