Thanks, that's helpful.
Just to address a couple of your points... there is a plan to let you use a "normal" file system when you use the downloadable version of the editor, as opposed to the virtual file system that you have now. So you won't need to download your code files, they will be saved on your hard drive like normal files that you can edit with WebStorm, Notepad++ or whatever, while still having the ability to use the Wade editor for editing scenes etc.
This is planned for version 4.2, so not that far off but realistically a month or two away.
Size-wise, I see what you mean. Generally though,Wade has been built with the idea that the one JS file you need to include (the minified wade.js) should only contain the core functionality that most games always need. The rest can be included separately (the physics engine, specific behaviors and so on). The core part is currently around 340KB, but only about 80KB when g-zipped (this is the actual download size).
In the past we used to do this to a greater extent, so for example the isometric part of the engine was separate from the rest. While this allowed us to shave off a few KB from the total size, in retrospect it wasn't worth all the additional complications. So now we have a slightly bigger core, but it does more of the things that you might need in many common cases.
I agree with your comments regarding standard display sizes. We do have a very solid scaling system, but it's not immediately obvious to users what they should do with Min Screen Size, Max Screen Size and all that. Could be made more intuitive.