Overboy I went back and read through your whole suggestion. I agree with a lot of it.
Arrow management, definitely.
Conditions in the node options so they can transition automatically if condition is true, hell yes.
Nodes with multiple inputs, I'm pretty sure it can already do that.
A few different node types like link to other flowchart, random, and potentially sequence, yes
I just don't like each node having it's own event sheet. I think it would encourage spreading logic around too thin, which would make issues harder to debug. If Scirra decides to implement that then cool, I won't complain, but I won't use it either.