I really like the junctions because having wires pass under nodes just messes with my mind. I think they'd be even more helpful if I could assign a name/label to them so when I mouse over them a tool-tip pops up with that name/label. I know some will cringe (I do!) at the sight of this but it is an example of where I'd use the feature
Yes, expanding the area used and employing link nodes would be helpful but I'd also like the option of labeling the junctions and it seems to me that it would be trivial to implement this request.
When you select multiple nodes, we also highlight any wires between them. This can make it easier to follow a flow once you have selected it.
This would only go a tiny way towards @LosinIt's suggestion, but is it possible that if you select the nodes at either end of a wire, the wire is highlighted even if there is a junction between them?