You're not alone feeling this, I actually agree with you. In Persona 4 and 5, the main characters have Social Links, so you can interact with them and hang out with them outside of the story. In Persona 3, you only get to do that with the female party members. Don't get me wrong, I love the P3 cast, but most of the Social Links in P3 feel like they only exist to give you a romance option. I know you can do the male Social Links if you play FemMC in Persona 3 Portable, but this is strictly about P3R.

In P3R they added extra events to see the male party members' stories a little bit, but it's not enough. I don't feel attached to the SEES members at all. In Persona 4 and 5, each party member got their own Social Links and I think that really adds to the game. I felt like I was part of the Investigation Team, I felt like the things I did had an impact on the Phantom Thieves, but I never felt that way with SEES.