To be honest I'd like it if the social links were ingrained better in the main story but I never really like that you have to do them to unlock actual content, like with Marie.
It actually reminds me of games like Mass Effect or Fallout where I had to change my playstyle just so I could prioritize the Charisma perks because I didn't want to miss out on any the ability of making the decisions that I actually want to make.
The most feasible way of weaving the S-links through the story would be to have some small callbacks to a S-link here in there.
For example: You're talking with the gang during the main story and if you've ranked up Ryuji to rank 3 he'll make a small joke referencing the S-link between the normal dialougue.
This way seems pretty neat and will also be feasibly possible to implement in the game.
Anyhow, we don't even know how S-links are going to work in P5, I'm sure they'll improve it a bit as the "S-links Vs Main Story" complaint is pretty common.
agreed, the fact that s-links are almost never referenced in the main story unless it's at the most climactic moment of the game or something sucks