A lot of good ideas, indeed. Here are some initial thoughts based on a quick browse.
First of all, I wish there was a way to run Boxer, to see the ideas in action!
I'm personally not a big fan of visual programming (I think it makes the high-ceiling of an environment lower, and the wide-walls narrower). But there's an argument to be made that it provides a lower floor.
So how can these ideas make Kojo better?
We need to make the workings of programs more visible to users. An important effort in this direction is the script-tracing GSOC project that's being done this summer.
We need better syntax-error recovery (these don't happen at all in a Visual Programming Environment).
I was also struck by the similarity, in a lot of respects, between Boxes in Boxer and Pictures in Kojo. It might be an interesting idea to slap on a nice UI over pictures to see where that leads.
In any case, thanks for the very interesting links!