Here's my wishlist: completely keyboard-driven; automatic graph layout; constraint editing to tree/DAG/full graph; don't allow connecting incompatible types; declutter by showing only N neighbours from current node; support for extensions to integrate different programming languages. Sure it's a tall order, but this is the building platform for future of computing :)
Since this thread is about Nodes, I'll try to give some constructive criticism. Seems like too much manual work is needed to organize the code on screen. Non-trivial programs become entangled because of 2D plane constraint. It's somewhat unjustified criticism though, since text programs also require lot of manual arranging ("architecture") and easily become hard to read. I like the built-in visualization of processed data. Cool stuff.