It would be quite logical. Compare it with real estate. Your primary location is your homepage -which normally will list your most important & interesting content. As you normally cannot put everything on your home, you shift less important content to level 2, and then 3 ..etc. The deeper the content - the less important you find it. So it's quite normal that Google follows this logic as well.
The second part is the number of internal links - because your most important content will receive a lot of internal links. Normally - the more links a piece of content receives, the closer it will be to the homepage (chances are bigger it receives links from the home, level 2 or level 3 content).
Index pages can help to move your content closer to the home - but this will only get you so far (this doesn't change a lot to the number of links these articles receive).
You could try to regroup your content in a cluster per theme - with it's own homepage & a lot on links inside the cluster to create more internal (theme based links) & move content closer to the home. There is an interesting post on this topic from Gianluca Fiorelli: http://moz.com/blog/topical-hubs-whiteboard-friday
Hope this helps,
Dirk