The Nautiloid crashes in the mountains. You and a few other survive without the Tadpole. (no Timer) You find a village and must stay because the mountain pass is blocked with snow for a few weeks. To repay and stay in the village, you slay monsters in the vicinity. Over time (Quests and Sleep) the snow melt, the people assemble a caravan for trade. You make a last Quest because in 3 days the caravan starts. You come back, a XXX attacked the village. Village people and not used companions are kidnapped. A ruthless organisation used the free mountain pass to invade because the Nautiloid promises treasures. YOu fight against the rearguard and now follows the Kidnappers... Act2
Thats my aapproach and maybe more in Gray Ghost taste.
No tadpole? Then why did the mind flayers kidnap you? Why the Nautiloid?
Baldur's Gate games, always started with a feeling of being hunted, or being in danger because of what you are, and 3 just does something similar, albeit in a different manner. We still don't know what the story has in store for us, and what other... curious abilities we might have.
I don't think i would change anything.
The narrative problems i hear about here and there, existed in the older games, and in a lot of actual tabletop adventures as well.
If you try hard enough, you can deconsruct and dissassemble anything.