Maybe it's just because failed romances that become strong friendships are something I've always found heartwarming (my roommate is still really close with his ex-wife and I've always found it so sweet,) but I like the idea of Hisao eventually taking Misha's place as Shizune's best friend in a post-bad end scenario.
Something like: Hisao and Shizune came back together as friends after some time avoiding each other (perhaps as a result of Hisao retaining his friendships with Akira, Lilly and Hideaki and eventually encountering Shizune at Lilly's wedding or Hideaki's graduation or something.) They wound up going into the same field, and became co-workers/drinking buddies/whatever, and since neither of them has ever really been good at forming new friendships, they reforge this sort of shared emotional dependency on each other, dealing with their feelings in their own idiosyncratic way--sort of like a Seinfeld/Elaine or Dante Hicks/Randall Graves thing, but played more seriously. They drink together and discuss their relationships (of which all eventually meet disaster,) and just generally act as wingmen to each other.
But then, let's say, Shizune finds love with the right person--somebody who is honestly and truly perfect for her--and Hisao finds that his best friend is drifting away from him, and realizes that for all the effort he's put into his life still hasn't made him any less alienated from others than he was on the first day he met Shizune. He loves Shizune, but they've long since borked their chances at being anything more than best friends, and after everything they've been through, Hisao realizes that he's finally in the position that Misha was in during the route; isolated, and seeing the person they love truly drifting away. And he has to reconcile his happiness for Shizune with his fears that, all along, he's been using her as a crutch, and without her, he can see how unfulfilling a life he wound up making for himself.
...Or something like that. I guess that's not really a BEFF so much as it's a Reconciliation-style fic for Shizune's route. But it's the only Shizune-centric fic I'd ever write.