Hi-
Could you clarify what exactly is not compatible between custom models and MB Relationships? It seems like the relationships table is mostly storing ID => ID mappings, so that seems like it ought to be possible with custom models as well -- is there something specific that doesn't work?
I'm building a new site and trying to figure out whether I can switch to custom models instead of CPTs for my post types that are only used on the admin end (do not need to have permalink/web pages). But I do need relationship support.