I know I am probably in the minority on this, but I like the idea of marking the solar systems that have anything of interest in them with system defenses. You might still have minor side quests or other things other than just resources in "unmarked" systems, but nothing necessary. Anything you might find in an unmarked system (marked by the fact that any level of system defense anywhere in a system marks a solar system as defended on the hyperspace transit map) is not necessary to complete the game.
This leaves exploration a factor in the game, while at the same time sorting through the huge amount of the "white noise" associated with a very large galactic map. Possibly very, very large if using the different map levels like magnifying glasses of the map levels below them. This creates a massively huge "galaxy" (or "Octant" of the galaxy, as us SFU players would say) for purposes of later expansion, and to give the player the sensation of being in a massive galaxy, but at the same time makes that "galaxy" small and easy to understand because places of importance, or another way of saying it is populated systems, are indicated on the galactic map by the presence of defenses.
This combination of things, dividing the full map into 4 levels of magnification and marking the populated solar systems, essentially lets you have both things at once. The map is huge, but the player does not get lost in it. They can easily move around it with the different methods of travel (hyperspace & quasispace), can easily understand it, and knows where anything "major" and important is just by looking at the map. Where the "populated and relevant" areas are, and where the "un-populated and uncharted" areas are that are unlikely to contain anything relevant to the story taking place in the populated area of the galaxy... unless a quest has led you there.
This all works very well and also feels like Star Control too me. As always, like any idea, this might not work with the game they are actually making. But, if it does, the more I think of all this the more I like it.