Hi, yeahjim,
First, thanks a lot, glad you're having fun!
Now, a lot of good has already been said here, but I'd like to address a few points:
Auto-Explore:
For a start, auto explore does have a few flaws, but not as many as you might think. For a start, it's meant specifically to *not* be omniscient. It is just as clueless as you about unexplored areas. Also, when in space, the auto-explore doesn't work with other ships around. That's your job (as the captain)
Gnashers: yeah, they like your shuttle for some reason. Use that knowledge accordingly
Bio-filter underground: unsure. will check. Must be an oxy-atmo planet.
Alien ship behavior: Each race has its own behavior. Gruff are dangerous until you win their respect, while monks and unifiers start out friendly. Once you start taking sides in quests, you'll really begin to see some interactions...
Ships for sale: yep, they just keep getting better, the longer you play.
Trading Mechanic: I never played it much myself, until I found out how much others used it and liked it. I guess I can understand the turn-based aspect of your thoughts, but all that stuff does happen, and if you miss it, you miss it.
Note-Taking System:
This has been suggested in one form or another several times. I will judge interest and work vs. reward over time...
Again, thanks,
Bob