Could be accomplished with local gates between hub systems with lots of space in between, or by having wormholes the player can discover. Or both.
Yeah, those are my thoughts atm, with the possibility of re-activating the Domain gates for really huge jumps later- kind of like what you were saying, it wouldn't get rid of all the traveling, it'd just bring it down to a reasonable level.
That said, I didn't really care for that aspect of Morrowind and I don't think they got the balance right. After a while, it was like, "wow, I have to cross the whole place... again???".
I'm firmly on the side of the players who just wanted to skip the whole thing. I've played enough RPGs with pointless walking around, I hate having my time wasted. I really loathe the JRPG habit of dumping us into forced encounters every 15 seconds.
If it's not as relatively-interesting as it was in Fallout (I,II) it needs a Skip Button somewhere or I get annoyed. And, since we're talking about RNG-generated Systems here for the most part... what's to see? I suppose that's a whole 'nother can of worms, though, and one that needs to wait until this part of the framework's in place.
Call it a short attention span if you want, I just don't care for games wasting my days "to experience traveling". If I want to experience travel, I'll put gas in the car and take a road trip. If I'm playing a video game, and there's traveling, it needs to have a point.
Regarding cost being near zero. You're not gonna be hauling 3 battleships across the sector on a whim, it simply won't happen.
If it can't happen, how are we supposed to create our 4X empires or explore the dangerous regions? In all seriousness, I think it's going to have to go that way; otherwise you're left with supposedly-awesome gameplay running an empire or exploring the galaxy or being a trader... but you can't actually do much, because half the stuff is too far away and too dangerous to ever reach.
This is also a potential game-wrecker, too; if the process is dangerous enough, people are going to be forced to stay in their starting System and grind for days before they've finally gotten the macguffin that allows them to get anywhere. They'll be complaining about how hard it is to merely get out of the System and videos of the leet going into the Far Reaches while they're frustrated won't help.
This can be mitigated by how the Sector's designed, for example by having a "danger index" for areas, and making sure that players always start in an area with a low "danger index" (something I intend to prototype when the tools exist, like my prototype for dynamic Systems last year), but once again, we're talking about wide swaths where, yes, players will travel around with fleets that are wreckers.
If it takes much time at all, then we're back to boredom. Hence why I brought this up; the long-term implications are pretty big. Doesn't need to be addressed in 0.6, heck, it's more than likely that the modders here will invent all of the mechanical variations on this that anybody could want within a month of its release, giving us all time to see what works and what doesn't. Just needs some thinking, in terms of the longer-term implications of the original premise- a thousand Systems, maybe 100,000 different worlds. It's a big number with big implications.