3- If someone deletes their sent messages, it should not affect my inbox.
4- Add more than one web link?
5- Auto Complete Twitter handle; for example when i start writing a tweet and want to mention someone; It gives me suggestions of the people I’m following. e.g. I write @shu it gives me suggestion of the rest according to people I follow and their handle starts with “shu” in this case @shusmo . this feature available in some Twitter applications.
The following were added by Ghassan Yonis in comments:
6. numbers of new “mentioned” (or at least notification that there is new mentioned) instead of having to click on the link and go to the “mentioned” page.
7. Integration with 3rd party sites within twitter.com itself
8. Mutual followers (like the mutual friends on Facebook)
9. To know if a person following you (other than try and send him DM)
10. RT with edit link, not just the new RT function.
11. If someone with protected feed mentioned you, you SHOULD see his tweet. He’s talking about you after all!