Nah. It's not Jay's fault.
The Beyoncé-JayZ partnership has been one of the greatest power moves in entertainment history.
The minute she got with Jay, she got a lot of media push as a sex symbol and iconic talent. He got her to stop making interviews (she loses mystique the minutes she talks without a script), he helped her team hunt for the best beats/songs( Amerie's beat which became Crazy In Love for example).
Before she got with Jay, she was one of the hot rnb girls. After Jay, she became THE girl.
I think Popular Music has moved away from the RnB formula. There used to be an Rnb song, Rock song, Hip Hop song and and Pop song in the top 10 between 1990 and 2009.
Since then Hip Hop has absorbed every single of them or just eclipsed it. Her team saw the trend and moved om with the times.
Im my opinion, if she stayed doing Irreplaceables and Upgrades she would have fallen of even more.
Look at the Shelf life of everyone who was her peer back then(2001). Who's still it?
Yes, Maybe her Dad brought something special to her craft but Jay's presence took her to an iconic level.