i like the atmosphere the tree creates. i don't know what dragon trees are for in the world of the movie. dragons seem to have the need to be protected somehow and the trees in front of the caves kind of give away where dragons live so they seem to be a bit of a security problem. but to me it's fun to wonder about such stuff and i don't immediately see it as a flaw.

yes, now that you say it, the timing of the cave collapse really is a bit strange. but if you are nitpicky you can can find such things in almost any movie.

all in all i agree with you that the story is a bit too choppy and could have been told with more flow if the movie had been a few minutes longer.