So for someone who hasn't played this since we had a server with Avali on it (the fluffy space raptor guys, as twi's personal text said once) and doesn't want to dig through the complaining and the arg and the chucklefish nonsense, is this worth trying again, and how much different is it from back then?
I'd recommend giving it a shot. There's an introductory mission now, something actually resembling a plot, no more sector nonsense. You can upgrade your ship and find crew for it. You can get randomly generated quests from NPCs on planets and create your own colonies. If you like modding, there's plenty of that going on. There is even Steam Workshop support in case you hate the Chucklefish forums.
It's far from perfect, but it's a good time-waster and not at all the sign of the apocalypse that some have made it out to be.
(The Avali you mentioned are in the Workshop as well, they're pretty cool and even spawn as NPCs.)