the problem is that even if the two players share the saves, when they continue on their own, they make decisions for their own, and get drop for their own that the other player maybe doesnt have...
You're contradicting yourself here, or at least being selfish.
Either you want to play in co-op and share the experience together, or else you want to advance in single-player on your own. It doesn't really sound fair to the other player to play a game co-op together, intending to play from start to finish, but then go off on your own and do something else.
What were you planning to so to your co-op partner. "Sorry, I got bored, but you can pick up my game a few hours later. I had some good adventures on my own, I'll fill you in."
If you want to play together, then play together.
So assuming you're hosting, save at the end of your session, and then stop. Don't play that co-op saved game any further in single-player. Instead, create a different profile. If you want to keep that character for single-player play, then copy the co-op profile saves into your new profile directory, and play that single-player character all you want.
When your buddy is available for co-op again, switch profiles and pick up the co-op game exactly where you left off. No, you won't have the exact same adventure - but that's the point, isn't it? To play with your buddy?
