The name change is final, I get it. So this is the last opinion I will express on this subject, but I hope it will at least be considered.
I slept on the name change, and today, I was thinking about why it made me so uncomfortable. I realized it had nothing to do with my having grown familiar with the old name. It had everything to do with the connotations of each name, and what it evokes on first impression.
Starfarer
When I first heard this name, immediately I thought about possibilities and adventure. Without knowing anything about the game, I could imagine a lone starship pilot seeking his fortune between the stars, or perhaps a captain and his crew wandering the far reaches of space in search of adventure.
It's a name that instantly involves the player in your story. "Starfarer...like seafarer, except in space...adventures of the high seas in space! Awesome!"
Starsector
When I first hear the name Starsector, immediately I think about a particular sector of space. Even knowing what I do about the game, I can't tear myself from the notion that something happens in that sector of space which makes it worthy of being the game title. So I feel like I'm about to be told a story. "Starsector is a location. So something must be really important about this location, perhaps a really good story happened in this sector of space!"
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So in conclusion, my own impression on this matter is that the name Starfarer evokes the kind of first impression that corresponds with what kind of game this will be, whereas Starsector sounds almost like a space opera, a kind of single play-through RPG like Mass Effect. Starfarer is a person, and that person is the target audience, the player. When you hear Starfarer, you know that YOU are the starfarer. Starsector sounds like a generic location in space. While it piques curiosity about what is so important about that location in space, it doesn't cause the player to identify so strongly with the title, because you haven't yet told them why they should care about that particular Starsector.
I wonder if anyone else had the same first impressions when they came across each name?