Could we include some kind of module (Probably 3600+ scale) that allows us to actually create a gravity well? It'd have to be a station-type module or hull (So no wandering gravity wells) that generates gravitational force around itself. It would act as a system, with its' size and gravitational strength dependent on scale * size. Basically, the purpose of it would act as a deepspace anchor (Such as in the big gulfs between clusters, or to act as a kind of 'interdiction sphere' defending a straight line approach from an enemy system, for example) with the possibility for another module that actually prevents jump drives in its' area, and perhaps even effects all ships that enter it with a huge deceleration (When entering field, reduce velocity by 9/10ths) that allows it to actually effectively interdict long-range attacks. The scalability would allow you to do everything from an anchored deepspace fortress/construction yard to a warp lane 'checkpoint' that stops ships from 'slowboating' into your system. I'm not certain how you would like to handle jumping 'through' the influence of it, if it would pull a ship out of warp, and the like, but I feel it would add a layer of strategic depth.
I don't know about anyone else, but I love making use of the empty space between stars, or clusters of stars, to anchor factories and artillery outposts, to tightly constrain the areas the enemy can move unseen, or to amplify the number of places I can easily access, but I've always been annoyed by the fact that, though my jump drive ships can jump FROM the base, they cannot jump back to it, meaning I either keep a force stationed there, permanently, at all times, or I trust my fixed defenses.