Thanks! The "incoming message" bug is a known issue with the 0.10a beta from earlier this week. The version I released today should fix that.
Conquest is a little easier/harder now, depending on stage. Large planets got buffed, but so did big ships, so it depends on what you're attacking.
I like the build room layer because of the way it alters the look and feel of the surrounding areas. That will become more important as the station graphics get better though. It's also a bitch to change at this point, so it's here to stay.
NPC's are currently purely self-interested (though your reputation will decrease if you raid instead of conquering, because that's seen as the sort of thing a lawless pirate would do). That also might change in the future, but it kind of depends on where the priorities land.
Lighter options are on the list, but they're a bit of a slog for me to write because they're not really my preference. I'll likely get to them eventually, but it may be a while unless there is a crazy amount of demand. Whenever mod support gets added though, you'll be able to make your own, which might help some.