A question that always bugged me, even with the gravity forming the jump points theory, is what determines where the nodes lead?
Well, distance in subspace is non-relativistic (at least, the physics are, so I presume distance must be truncated too.. or time, perhaps. Nuts. That's not really an answer, then.....), so it could be the nodes are right next to each other in subspace itself. IIRC nodes are described as being points where 'the fabric of subspace is strong enough to support subspace travel'; perhaps gravity has a role in directing those 'strands'; y'know, if a subspace connection is like a piece of string of a particular strength, and gravitational effect at each end drags and locks that strand-thing into position between the two apertures (perhaps the destruction of one end by the Lucifer/in FS2 being enough to weaken it and allow the strand to break free).
Of course, that itself has an issue of what causes apertures to form and collapse as well as the specific pairings; the former could be that these little apertures form naturally, but only remain open when there is sufficient gravity to 'snap' the strands into place (with the caveat that even stable nodes collapse; although perhaps stuff like natural movement of stars in subspace or realspace can strain and break connections over long time periods). The latter could be that it's just pot luck, in terms of relative subspace distance.
Absolutely no support or evidence for any of that, of course. Could be that gravity is somehow converted to energy in subspace and 2 simulataneous random subspace aperture formations in the right place allow said gravity to create a conduit of energy that strengthens subspace for travel. Or maybe you get a mini-black hole effect that pulls in atoms at either end and creates a tiny tunnel, which the travelling ships act to widen (as they do to the aperture when entering subspace).