1. Playing nice with version control. Opening a graph and moving a node by one pixel should cause not merge conflicts. Stop mixing logic and layout together.
2. Lossless round-tripping to a human-readable text format. Text editing tools are insanely powerful for many things. Not being able to use them is a huge drawback of node-based development
3. A common format that allows people to build tools that are agnostic to your specific environment. Node editors themselves should be like IDEs - not tied to a specific app. I don't use a different code editor when I switch from Godot to Unity - why is the node editor any different.
4. Just better everything. Batch/bulk changes, search/replace, auto-align. The quality of these essential features varies from "passable" to "what?"
Everyone is reinventing the wheel all the time. Every platform, app, environment has it's own way of editing node graphs. And most of them suck. The amount of wasted effort for mediocre outcomes...
Finally - are we sure node graphs are the best metaphor? Modifier stacks (like 3DS Max) give you 80% of what you want for many use-cases and they are a lot easier to learn and use.
Event grids are great for many things - and again they are much simpler.
Maybe node graphs should be the "expert mode" not the default (although the real "expert mode" is surely good old text coding - with all it's faults)