Improvement methodology...?

Hey guys,
I'm here because I'm working on a project that I've wanted for a couple years now, and ironically my job requested a similar project be completed. And so, I have begun designing a basic web site, which obviously needs some work done on it, but shows my "vision", more or less. I, personally, thought it looked fairly decent at the least - especially since it's not completed(Nav system/Banner & border integration).
However, I was told it was a "Fugly website". Fugly, as in.... [blank]-ing ugly.

The goal:
A Project Management system (as made obvious by the render @ bottom of post).

The coworker that mentioned it this way, I trust to no-end, and so if he say's it's ugly, then I'm positive it is, as he's very knowledgeable on web design.
The problem, is that I have no idea how to improve. I was hoping some of you guys could criticize (not too harshly I hope. Keep in mind I've already been told that the last 38 hours spent on this resulted in "Fugly", so I'm about as 'down' as it gets.) my project, or hopefully have some pointers as to how I can improve on it?

Any help/advice/criticism/comments/suggestions are greatly appreciated. Knowing why it's a bad design would be the first step in fixing it, I imagine.

Sincerely,
J.P.

--- Here's the Render: