Perhaps what you're seeing is co-op moving house to places like Global agenda and Firefall, where it becomes the (or at least a) central theme. It works better that way, because it always seems to feel a bit tacked-on if gameplay isn't designed around it. The trouble is that if you take what is essentially a single-player game and allow players to co-op, the whole dynamic of the game changes; Players' focus moves away from the game's story to the other player/s as they work to maximize their effectiveness as a team. This can be surprisingly challenging (at least in part because most players are woefully undisciplined, no matter how fervently they believe they're a highly-trained warrior), and having played through the game solo already won't exactly help keep their attention focussed elsewhere.
Designing multi-player games is very different from designing single-player storylines (See what I did there?), so if you're looking for multi-player, single-player games are probably the wrong place to look. That doesn't mean that more couldn't be done in the hybrid multi-player storyline area, but co-op mode really has to be tailored to a multi-player experience, which often results in something that looks more like an MMO, and after all, since AI is a factor, wouldn't you and your buddy rather team up against the great unwashed than face the same old bunch of brainless NPC mobs?