1) Making it easier to compose Tweetstorms (third-party services like WriteRack exist, but it would be nice to have official support).
2) Enhancing the display of Tweetstorms to make them easier to follow. Right now, the UI for viewing Tweet replies is the same regardless of who's replying to who. Twitter could make it so that a person's replies to themselves (the building blocks of a Tweetstorm) have a unique look-and-feel compared to replies from followers. This would emphasize the Tweetstorm as a distinct type of posting, rather than something jury-rigged out of self-replies.
3) Not Tweetstorm specific, but make it easier to have and follow branched conversations. Sites like Reddit have this down already, while Facebook and Twitter seem reluctant to let anything go beyond one level down. Let people branch! It would actually make things easier to follow, and it would also allow for something (sort of) novel: branched Tweetstorms! Linear text is so 20th century! :)
The timeline thing is a real(ish) problem that can be solved with UI, in a similar way how they show conversations inline (automatically collapse them)