The notification manager will be nice when it is further developed. In the mean time, I am tempted to use thoughtful but counter-intuitive plugins such as https://wordpress.org/plugins/so-clean-up-wp-seo/

I certainly appreciate the countless hours of Pro bono work that many plugin developers have contributed. The freemium model seems like a great marketing tool if used correctly. I agree with many of the previous comments - keep the advertising on the individual plugin settings page. I have unfortunately have been conditioned to ignore the nagging irrelevant admin notifications and accept the fact that screen real estate is compromised.