Hi, I'd like to offer a thought for v3 or beyond. One of the things that can be visually confusing in Node-RED complex flows is where wires cross each other.
May diagramming tools use the engineering drawing style "jump" where the wire visually has a small loop as in this example from Microsoft Visio.
The wire with the loop on it is generally the one with the highest Z value.
The challenge with this idea is the cost of implementation. We would have to calculate the intersection point of every wire whenever anything moved inorder to add this level of detail.
As it stands, we want to reduce the cost of rendering the flows, not increase it
The wires do have a white border which helps to some degree to show where they overlap. We could certainly explore tweaks to that to make it more apparent.
Some time in the last 20 years, while I wasn't looking, the common practice for this seems to have changed. Generally, wires that cross are assumed not to be connected unless there is a small "dot" or "blob" at the intersection. This probably happened, as @knolleary implies, to reduce the burden on circuit drawing and simulation software.
A good way to look at this might be that such crossings are just artifacts of how the editor displays the flow. They do not create any functionality, and so probably should not consume any resources in the editor or runtime. If old-timers like me are bothered by it, we can always re-draw the flow. The "younger generation" probably grew up with the new style and have no trouble.
It's OK on a white background, but would not look good in a 'group' with a coloured background... unless of course the border was colour keyed to the background.