It was definitely on of the best endings I've seen in a show . It tied up all the loose ends perfectly. Now I admit the commercials were annoying but I disagree with your other points.
The Risen thing was obvious but done well. They've used it throughout the series and has been their go to for stealth kills. Walt is a genius mastermind who is attentive to detais, of course he was going to notice that she used the same sugar brand everytime they met before. I even guessed that he put something in the sugar packet when I saw her reach for it , while it was obvious it was smart since the whole reason he even wanted to talk to her was to kill them. It would have been stupid if he took care of everyone at the cook site then had to escape the DEA to get rid of her.
As for Jesse I figured he wouldn't shoot walt, that would be playing into his plan and giving him what he wants. The dude has cancer, a bullet in his liver with the DEA coming after him and his only option is to kill himself. Those alone can cause way more suffering than just shooting a dead man.
Skylar is definitely paying for her mistakes, she lost her husband her son sees her as just a bad a person as he was. Plus all the other things haunting her conscious. They guy also said that she was on trial when walt was in his cabin in the beginning.
I liked the part when he scared his old colleagues, I can't believe they keep trying to make money off this guys life, what a couple of a**holes.