I don't disagree with your view of not taking him in the first, it's not unreasonable, but I think you are being a little bit harsh on his defensive game. Personally I like how little time he spends in his own zone. Contrary to what you saw, I typically notice that he is able to transition out of his own zone so easily that he doesn't spend much time hemmed into his own zone. I think he loses his angles in the defensive zone a little bit too easily and loses inside leverage. I think his pivots are still a bit sluggish and he needs to accelerate faster, but my concerns of his game revolve around his lack of strength and just getting a little bit faster and quicker on his feet. Once he gets bigger and faster, I think his defensive efficiency should improve.
You also bring up a good point about how he often plays with Sanheim. One point I will make is that Bean has been quite a bit better this year. Most of Bean's production in his 16 year-old season came as a result of short passes on the power play. He has upped his game and is a real leader on the PP - he carries the puck up (not Sanheim), and Bean has really looked more confident extending plays and managing the ice. It should be expected that any player will look better playing with top players. I had a couple concerns when I saw Brett Howden about how much heavy lifting Brayden Point did on that line to create opportunities for his linemates. I don't think that Bean is being "carried" as much as I found Howden to be when I saw him. Point is, you can expect any player to be more effective playing with better players. You can interpret it as a positive because you know they will be able to compliment and work with smarter, faster players at the next level, or a negative that their play is being elevated by stronger linemates.