Custom branding: while the option to custom brand what the customer sees when they open Team Viewer exists, the option to customize the program as a whole (like what Screen Connect does) does not. Team Viewer is not 100% white label, as you cannot change the program name, icon, or taskbar settings.
Annoying popups: we purchased the pro version of Team Viewer 12. The next month Team Viewer 13 came out. Since that day, we have gotten constant popups and emails offering us discounts to upgrade to the next level. Even after clicking the option to never show again, the annoying messages return within a day or two.
Two-factor authentication: perhaps a necessary evil? But who on earth is going to want to add a computer to our account if they are not being supported by us or have access to that account? Each time we add a new computer to our account, we must verify it through a link sent to our email, which we don't always have access to. It's an annoying and timely second step that should not be required.