Clannad, Seishun Buta Yarou wa Bunny Girl Senpai no Yume wo Minai Recommendations
The two series have a similar structure and the main characters share a similar role. Also both series integrate the supernatural into an otherwise "real" world to a surprising degree.
-Same main character at the beginning of the animated as Tomoya who is seen a little less like an outcast, but as a single person with only one or two friends.
-The main female character is very different from Nagissa in her attitude but she is in the same situation, a lonely girl, who is also the senpai of the main character.
The character who disappears from the sight of others, is reminiscent of the story of Fuko Ibuki in clannad.
Character-wise and dialog-wise and teenage-problem-connected-with-some-supernatural-stuff-theme-wise there are many anime out there that are more like "Rascal Does Not Dream of Bunny Girl Senpai" but - BUT - I got an almost mystical feeling from "Clannad" and I got a little bit of the same feeling from "Rascal Does Not Dream of Bunny Girl Senpai", so I think the reason, why both anime are so popular is made of the same essence and if you liked one I recommend to watch the other to maybe find this essence again.
Both MC kinda the same.. a rascal, and also an outcast.
Both MC are chick magnets, not all girls are involved romantically, but certainly these MCs attract lots of troubled girls.
Both have disappeared from existence girls.