Yeah, I feel like Makoto is just... lacking something. We've already had the "strict student council president girl with a lot of pressure on her shoulders" character in P3, and to be honest, Mitsuru still did it better.
That's not to say I hate Makoto, I still like her enough, but after playing through the game once, everyone else is more memorable than she is.
You know that part where you have to go run around giving a pep talk to all of your team members in the Velvet Room toward the end of the game? Yeah, I ran around for a while because I got everyone else but totally forgot that Makoto existed