Off the top of my mind tagging is also a weak spot (it insists on users using one of a number of defined tags, and while tags can be added it takes time and you also cannot type them out but have to rely on clumsy nested dropdows for all but the top 10 that can be reached via keyboard shortcuts.)

I'm fairly certain there was more problems but all in all OneNote still used to be a good solutions for smaller companies that was stuck in Microsoft land anyway.