Chrome "New Tab Page" not showing most frequently visited pages

Chrome not storing history is the problem, the most visited websites are based on how often they come up in your history. If you are intentionally blocking chrome from storing your history then try turning your history on and visiting the sites you want on the new tab page then turning it off again(I do not know how to turn it on or off on command). If its unintentional then it seems like that would be your main problem.

• Go to Settings, in Google Chrome.
• Then, click on Show advanced settings.
• At the very end, you will see Reset browsing settings.

Click on that: it will change to the default settings, but hey, it will also clear your browsing history and disable extensions. For extensions, you can enable it again if you have installed them like ad block plus or any other.

Hope that answers your question.