Much of Fallout 4's problems come down to the fact that the engine does not handle shadows very well at all. It wasn't built for it, even though it has been heavily modified over the years. The biggest fps hits in the game that I remember are when you're in the city where the buildings cause zones of bright sunlight and deep shadow all around you, and spotlights. Spotlights used to be terrible if you had an older/weaker PC but they've actually much improved that by patching. Still, I always shot them out.
The other unique factor Fallout 4 has to deal with is the extreme amount of player interaction with objects in the world. The game has to remember and deal with all of that. I can't think of anything even remotely close. Skyrim is a drop in the bucket in comparison and it had so much going on that the PS3 couldn't deal with it late-game. It's really a game that shines best on a solid PC.
I suppose it's time for a new engine, though I'm kind of dreading that. Mod generation will be knocked back to square-one and development time will be extended greatly. I don't give a damn about the graphics but I think they ran into a wall with the engine in terms of doing stuff they wanted to accomplish.
