What needs to happen really is that the Fresh Section needs to get closer to reader's attention. As many people know, the Fresh Section is thrown so far back that it's all but impossible to make impact there. You need to advertise and all that just to get attention.
Let's look at that front page. You have this massive Spotlight, which, while the size could be smaller, is fine. You want to promote our popular work. Then underneath that you have the big App banner which frankly, could be condensed and put on the side. After that you get the Top 10 Popular Comics and Top 10 Popular Novels. Then you get two layers of Popular Comics. Then you have this massive advertisement. Afterwards you get a section for Premium Comics and then a section for Premium Novels.
Only when you get past all of this do you reach the New and Noteworthy Comics and Novels and I'm not sure if that's even technically considered Fresh. If it isn't then you go to go straight to the bottom of the page before you reach Fresh. Even the easier path of just clicking on Comic/Novel still requires you then to go over to Fresh.
It's understandable to want to promote the popular series but many people know how difficult it is to get attention here unless its given. There was a whole topic on this about how some series struggle to get in the limelight. Other sites have implemented this idea far better I feel.
Quite frankly, just do what Smackjeeves does in terms of design.You can still have your Spotlight at the top. But then have Popular, Fresh, and all that in the same line of sight. If you wish you can have Popular focused on in general. Again it's fair to want to promote your best work for the site.
In the end you still put emphasis on the popular work but now Fresh and New isn't so far back you got to go on a mini-adventure to find it. It's there, closer to your attention and the closer that is, well the more likely I feel you are to click on it.