I've never played the Ryujin quest. Seems like that's a good thing.
The only annoying bug I'm encountering on my current run is the vanishing inventory thing when I steal enemy ships on the ground. It's happened a couple of times now. I don't want the glitch to take hold, so I just go back to the quicksave I always make before trying and don't do it. I still have no issues getting the ones in space, which is more fun anyway.
And my character occasionally stays invisible. The NPCs and followers still interact with him, but he doesn't show up. It's kind of funny. When he sits down in the cockpit pilot seat, the helmet is empty.
I haven't done a single complex quest. I occasionally gather up an artifact or visit a temple, but other than that, I just kill pirates, take their shit, and build ships and (non-linked) outposts. That's what I enjoy and it works for me, and for the most part I don't encounter the buggy crap that makes me crazy.