Understanding user experience doesn't mean you're paid to nit about every little thing. Understanding a user experience designer means trusting in their abilities and value in web application development when putting effective human interaction into applications to make them usable and powerful.
Every so often something reminds me of a point in my career where a colleague approached me. He had been heading up this super top-secret project that was supposed to change everything. His question to me was, "How many flyout menus is too much." My reply to him was, "One."
Think about that. Maybe they start with a hover-activated pulldown, which is usually necessary. (However, I prefer there to be none of those either.) From that pulldown, you're directed to hover more to view more options. Part of the issue is that you're directed to be precise and balanced with your mouse. It feels like you're being forced to do yoga. The more flyouts there are, the more it turns into a maze where you can't touch the sides.
The other part of this is a content thing. It used to be that there was never enough content. This was the time of transition to the Internet, where everyone wanted a webpage but no one ever knew what to put there once they got one. Now the simpler the page, the easier it is for someone to use… the more your viewers understand what's going on. Understand that unless your site is actually a book, you don't really need every single detail accessible by the nav.
There is a balance in content that needs to be maintained between four areas: Marketing, SEO, usability, and the business. To achieve this, there needs to be good communication and understanding between these areas. Minimizing or combining content makes good sense anyway, even without the fact that it will minimize the need for flyouts.
In the context of complex applications, it's always best to guide your users through your application. Wizard-style isn't always a good idea, but it's more usable than flyouts. It doesn't hurt to at least combine similar functions or group your functions into segue pages. Consider giving your power users the ability to bring the functions of the application they use most to the front in a sorta dashboard-style interface.
The project that my colleague was working on ended up having one level of flyouts that, in my opinion, could still have been avoided to ensure a better user experience. But I still like him anyway.