Tree is there already (in last version separator position is set to 0 because it doesn't work yet but it presentsHaving a tree like and a branch like presentation options.

Branch view... maybe... in future versions...
Please describe it with details (I can't understand it).Ability to flag/filter if "link" come from script or by manual operation.
Option to visually select/see dependent script from the explorer
You need to load script to a new folder and open explorer at that folder. Explorers and TC works with same VP. You may write a simple script that will do it.Ability to load a saved filelist in the explorer to use with current VP.

Why? Links and scripts may be dragged already.-> Bug/limitation
it is not possible to drag from oneVP to another trough the explorer.
Virtual folders - yes, now can't (we need to enumerate entire contents and list it in drag data).
Another heavy task is to drag to external applications because we need to recreate structure in temporary folder (even if we're dragging a single file if its virtual name differs from real one) and specify path to that structure (drag data must contain physical paths). But I think I'll realize it.