Instead of a box-and-lines diagram, I think the stuff that people really want is:
- Structured editing. Valid change operations are obvious (maybe listed in a menu). No invalid states.
- Cross-cutting connections are explicitly displayed (with lines or arrows or etc) instead of being implicit.
- UI does a better job of highlighting just the relevant information and hiding everything else.
- Overall more simplicity. As in, I think some people imagine that their thousand-lines-of-code project could be fully represented as a few boxes and lines with labels. There's some unrealistic expectations tied up in this area. But simplicity is still a good goal.
Those are all good goals and there's different approaches to solve them. A lot of those asks can be solved by keeping the text document interface and adding enough cleverness on top of that (like EVE / LightTable). And there's other visual systems other than boxes-and-lines. People just need to think outside the box. (ha ha, sorry)