It's not all that difficult to do if you're smart about it. Every single combination doesn't need to be unique, after all. Chunk up the ending and make it modular and it shouldn't be a huge problem. For example, intro telling how the MC and the girls that stayed live together, with a layered image showing the group. Then a montage of small scenes showing MC with Rae, MC with Lyriel, etc. filtering out girls who didn't stay. Add some scenes with two of the girls who had a particularly strong relationship with each other into the mix. Then cap it off with another group shot. There's your ending. It's work, sure but not 64 times as much work.