While I appreciate that the developers were trying to still give access to the "Hot Questions" across the Stack Exchange network, I find that this solution is inadequate. The point of the list being accessible from the top navigation bar was that it was accessible from anywhere. Now, in order to view these questions, we have to navigate back to the home page. This sounds like a trivial thing to do, but the fact is that (for me, at least) it's quite out of the way.
For example, I have Stack Overflow bookmarked (like all the cool kids do). But I never, ever, ever actually visit the home page of Stack Overflow. My bookmark points only to the java questions (http://stackoverflow.com/questions/tagged/java?sort=newest&pagesize=15). Why? Because that's where my expertise lies. Looking at the home page of Stack Overflow is useless to me, because the vast majority of questions that are presented are things which I know nothing about, can't contribute meaningfully to, and likely can't even read just for entertainment value. So I spend my time on the Java side, where I can be of some value. And if ever some question was asked of some amazing worth, guess what? It would show up in my "Hot Questions" drop down at the top. Absolutely no need to ever view the master list of questions on the home page. And, frankly, I liked it that way.
Now I have no way to casually glance at these "Hot Questions", which I think is a fundamental flaw in the design of the navigation bar and will severely hurt not only the integration of the Stack Exchange but also its growth. I know that I, for one, have created profiles and become interested in other Stack Exchange sites because of the appearance of an interesting question on the "Hot Questions" list. Being able to glance at it and see what interesting things people are talking about is one of the core ways users from one site get visibility into all of the depth in the Stack Exchange network -- and in my opinion, Stack Overflow, as the largest member of the network and the parent of the whole organization, has a parental duty to do what it can to ensure this continued growth and development. I would have never heard about RPG.SE, Gaming.SE, CodeReview.SE, English.SE, or any of the other awesome sites that exist here except with the casual exposure to the "Hot Questions". And to be honest, if they had been just another ad-looking list on some trivial side bar, I probably would have never taken them seriously, anyway. We (Internet users) quickly associate information in sidebars as "irrelevant", "unimportant", and likely "uninteresting", because so often they are filled with ads or tertiary information.
Long story short: I really do love most of the new navigation bar, but your solution to the "Hot Questions" list is inadequate. Please bring it back onto the navigation menu, both for the ease of your users (customers) and for the future growth and health of the Stack Exchange network. To be perfectly honest, the "Hot Questions" list is what's kept me coming back to this website day after day. I love being able to glance at it once every half hour or so at work, just to see if someone is saying anything interesting, while I look through the Java questions for anything I might be able to help out with. By making it less accessible, it damages the experience of the site and reduces the feeling of community (and, of course, the addictive "keep coming back to see what's new" psychological feature of the site, which I'm sure the higher-ups insist doesn't exist and isn't part of their benevolent business model!).
I miss it.
Just one man's opinion, of course.