From a throwaway line in the ending, I assume we're supposed to find her embittered and flawed with smoking as a prop. But it doesn't really work.

You are correct that this was my intention. In an earlier version, the final scene had her smoking, because if she valued smoking, Princess Celestia wouldn't have copied the negative health effects. The paragraph didn't really help the scene so I cut it. Since you're the second person to find the smoking a turn off, I'll consider cutting it.

Can you suggest a nervous, compulsive tick? Tea doesn't strike me as a compulsion.

It's pretty good but somehow I feel a certain lack of narrative drive from chapter to chapter aside from the question of 'what will Celestia do next?'

This is probably an artifact of how it was written. Most of the chapters were disconnected scenes that I wrote, without much planning. Only early this year did I start taking the individual scenes and stitched them into a whole piece. (If I write another piece of medium to long form fiction, I'll make sure to not repeat this process; I'm not entirely happy with said process.)