Regarding the documentation, will emphasis be put on the AutoHotkey_L documentation? Keep in mind that the same source files are used for the CHM file and the online documentation. I'm not particularly attached to the current style, but I think bright green comments (or anything else) on bright cyan background doesn't really work.
I think a simple collapsible side bar would be good for the documentation. For example, one like MSDN's lightweight view. I'm not sure how much information it should show; the AutoHotkey documentation isn't nearly as hierarchal as MSDN.
just upon quick glance, the sub blue bar stands out to my eyes, and i have to really spend some time to realize that thats not the main menu to focus on, the black one is.