My current ExtJS application haves:

18 views
7 custom components
13 models
18 stores
13 controllers

Still relative small application but starts to be very difficult to navigate.
I do my server coding with eclipse and the difference why I have no problem navigating my java project is the use of packages ("namespaces") and tthe fact that eclipse's project explorer dont share (even if can) its area with another tool container.

eclipse:
ext1.jpg

SA:
ext2.jpg

I took this images in my laptop (1366 x 768). In bigger screen (I sometimes use SA at work where I have two 1920 x 1080 screens...) theres is no much problem but normally I use SA at home where I have no external monitor available.

A solution could be changing east region of SA to tab panel, one tab for project inspector and another for property inspector. Or move the property inspector to west region (you can do now that but component description stays at the bottom of the west region) and move the toolbox to the north region like Delphi 7. Newer versions of Delphi haves the "toolbox" where SA haves property inspector but there is a plugin which moves it to north region, for example:

ext3.jpg

On the other hand, controllers tend to have many "entries" (actions, basic functions and references) so a nice addition could be sub-nodes in controllers, one for actions, another for references and, of course, one for basic functions. Look a this controller, barely fist in the project inspector with toolbar hidden and property inspector reduced at maximum:

ext4.jpg

Regards.