It would be nice to have a bit more control over which messages are forwarded to my phone using twitter. Spam is fairy easy to avoid, but other kind of unwanted message come from a probem with twitter only having one stream of messages per user. 

I can see the use for clients like twhirl and other desktop clients to allow you to post and read in more flexible ways.  It would be nice to be able to do some more filtering and selecting online.  I can see an idea for an automated filter and repost tool, create a filtered or composite twitter feed to add to your friends to stay in touch if their usual feed is a bit busy.

It would be nice to be able to be a bit more selective about what you read and send using text messages. I find the text based interface the most useful one, but lacking in some selectivity.  You can follow or nofollow - that's it.  What if I want to follow everything except 'new blog post' twitters for example.  I hope paying for text message quotas may drive some development in this area.

It may be useful to look at other microblogging services like jaku, following their acquisition by google