Part of the problem, I suspect, is the script-based approach to handling "quests" or missions. I'm struggling with the same issues in Frayed Knights. To make things interesting, the entire sub-story and path to accomplish the quest is scripted out in advance, and any alternative approaches have to be similarly designed, tested, debugged, re-written, polished, and perfected.
But is this really necessary? Couldn't the Lord British approach still be applied to modern games? So you've got the glittery orb quest item stuck in some room. Is it really necessary to dictate how the player obtains the orb? Must all events and approaches be deliberately scripted into the game, or is it possible to set up a more generic event system and let things proceed more as a simulation? Would it be just as exciting? Just as interesting?
Yet even as I say this, I loved the hand-scripted resolution to the subplot where I acquired an alliance between the Umpani and T'Rang, and nuked the Black Ship. I'm a junkie for hand-crafted, well-designed plot and story development.
I'm sure I chose the most tedious, least interesting path to freeing the two prisoners, so would I be wrong in criticizing the game for allowing such tedious gameplay? Wouldn't I have enjoyed the game more following the nicely-scripted path?