I don't agree.
One of THE best feature about SR is, go-anywhere galaxy.
You can even have fleet meet in deep space.
I hate those warp-high-ways.
With that said.
It's easy enough to create a sub-system called "Warp Gate" and make objects that do not have Jump Drive to warp to other system (or arbitrarily point in space). In fact the standard game already have this, just not for building by player. Or you can modify the current Jump Drive to be able to target an object (with sub-system, mass, etc as restrictions).
It is *FRUSTRATING* to see ships with automation that does not use Jump Drive, but even that can be address with mods (See my Minister Mod as example, one of main reason I wrote it was to make Jump Drive more useful).