I've asked about this on HN before (whether others feel the same way). It makes me feel safer to use pivotal knowing they're going to charge for it.
* markdown (code blocks, anyone?)
* editing or deletion of comments
* grouping stories
* replying to comments by email
[Edit: list formatting]
http://skitch.com/benatkin/rkecs/pivotal-tracker-story-view
Also, why not have an expanded, non-editing view? The <input> elements do take up extra space when just viewing the extra fields.
It seems to me that they're missing some of the finer points of Single Page Application design. I wish I had a good guide I could point them to.
Again, though...they're totally nailing other parts of single-page application design. It's an amazing app that could be made a lot better with some refinement.