Even the best authors have to change their story back and forth before finalizing and publishing their work. But this is very difficult for an on going work. In the future, as the plot develops, when your story telling skills improve, and new ideas come up, you will wish you have handled part of the story differently. What do you do at that time?
There really isnt a "correct" answer for this. However, I'm worried because you seemed so eager to modify your original, core idea when the game is still at such early stage noone but you know the best for your story. I'm not telling you to ignore your audience but most people (including me) don't know what they want until they receive a product they love.
Now what do I think about the rework? I think your story telling skill has improved dramatically and the new plot is good. But I don't think the original plot is at any point "weird", or maybe its better to say you didn't have the skill or planning to tell the "unique" story at that time so people found it "weird".
