Although I'm somewhat hesitant to make overt comments about the respective quality issues, there are more (and newer) people involved in the making of D:OS2 so it may be that it's been harder to get a larger and geographically diverse team always singing from the same hymn sheet, at a guess. But I'm also reminded that the later stages of the "original Original Sin" also took some time to get quite right and the ending was significantly reworked, for instance.
Having said that, I haven't played OS2 to the end since its revamp, partly as I was so disappointed by Arx first time round: it felt more empty than Hiberheim and there were a few bits that were conspicuously unfinished (doesn't come much more conspicuous than saying "placeholder"!) plus some of the reworked lore made me feel slightly meh.
A lot of games end up with a community patch to iron out the various wrinkles, but I'm not sure the modding community is quite at that stage yet; again, that's more of an admission that I don't know rather than a comment that it isn't. What I think is a safe bet is that any community patch wouldn't need to be quite as grand in scope as those required for Bethsoft games.
