- Putting followers into categories (SEO, Web 2.0, yogis...) - there is "GroupTweet" but you have to ask everyone you want in each to join it. Laborious.
- Having the "search for people" tool actually work and not be out of service every time I try to use it
- Threads for replies (I can't always remember what the reply was about)
- Categorise users by "not following", "new", "long-timers"...
- Recommendations for people who I might be interested in following
- A filter for spam and fakes
There are external tools who allow you to do some of these things. I think it would be nice to have it all in Twitter though.
For a good list of Twitter tools, see the Seoptimise list.