Here are a series of diagrams showing some of the site analysis work that I have done in a more simplified style.
Aerial Image (I tried to reduce visual distractions by minimizing details and colors).
Figure Ground Digram
Figure Ground + Site Image
Mapping the Trees
Mapped Trees + Site Image
Public Transportation
Public Transportation + Site Image
Railroads (pretty simple, yet the most challenging characteristic of the site).
Railroads + Site Image
Combination of all studies done
Final Diagram + Site Image (maybe slightly harder to read. The individual diagrams convey the idea in a simpler way).
Biosynergies 
Baha, you did a nice job in mapping crucial elements. In the future, you can work with your classmates to split up the busywork and then you can spend more time on interpreting the graphics.
I liked your observation about the overlay being harder to understand than the single layers. The diagrams without the aerial could be read at a smaller scale due to their relative simplicity. Be careful about using the posterized aerial without editing it: the jagged shadows and 2nd to lightest grey value shapes are actually distracting noise. You could smooth the shadows and perhaps delete the light grey shapes that have little meaning. Add a little orange to the yellow and it will be more legible against white.
It would be good if your blogposts tell what you think about the site now that you have mapped it. For example, I was surprised to see that there is actually quite a bit of tree canopy since they are so overwhelmed by the building masses.
You could also compare how different urban designs for the Lloyd area would affect your site.
Please note that your 12.5 MB file can be optimized to 3.3 MB (use Adobe Acrobat Pro > Advanced > PDF Optimizer).