Personally I'd like to see some of the non-vanilla house systems that currently seem to serve little purpose removed or cut off, and their assets moved into the primary systems. Systems like Virginia, New Hampshire, Ontario, Alberta, Puerto Rico, Vespucci, Tottori, Nagano, Thuringia, Cologne... just as some examples.
These systems, IMO, are kind of a no man's land especially for newer players (or players returning after having not been around for their implementation, or not having played since vanilla FL). A lot of people are accustomed to the core vanilla FL systems, and when you have a bunch of systems that are off the beaten path and often inaccessible except by wayward jump holes or tacked on gates, it becomes confusing to people.
I'll admit I'm one of those people, after returning to disco, having not played since 2009, most of these systems are completely foreign to me, and if it weren't for the nav map utility I probably wouldnt even know most of them exist, nor have any reason to go there.
The important assets from these places can be moved into recognizable systems as needed.