Another prob with using the wormhole mechanics for jumpgates would be that the wormhole does disappear after one ride...not sure if you could make it permanent by modding only.
I haven't tried this (yet), but you might be able to use the wormhole effect as a triggered event activated at a starbase. I'm not sure which trigger would work... I'm fairly confident there is an OnConstructStarbase, but I'm not sure about a trigger for modules...
If you could specify some coordinates or a direction and distance as parameters to that action that would be really great, but for that to come true we can only hope ...
The other problem with coordinates is that everything that can be given coordinates, as far as I know, can only be given coordinates in the xml, not from player input. Unless I've missed something, there is no way to feed coordinates to a triggered event dynamically.