Actually, no. Yellow means that a tweet is a reply. Blue is the default colour meaning a normal tweet (which may be a start of a thread). But, yes, the idea you had is correct. (The origin of this colour scheme is Jaiku.)

There is a small star on the top-left corner of a favoried tweet in Mauku 2.0 (the star was on right side in old Mauku 0.x).

This was considered when designing the new Mauku 2.0 UI. However, there are couple of issues with tree style views in Mauku and Fremantle.

First, the depth of a such tree could be anything. There would be a single first tweet, but after that tweets could be nested very deeply, since replies may have replies also. (Jaiku prevents this and have actually a concept of a thread, but Twitter does not.) If every level were intended, let's say, 20 pixels, only after few levels, the message area would be very narrow.

Secondly, Mauku is built on the concept of timeline. The latest tweets are always on the top of the window. If tweets were grouped into threads, it would be much harder to find latest tweets, since an user had to browse all active threads to read new comments.

Thirdly, the Fremantle HIG does not encourage to use of nested tree style lists. I can see why. Instead, subwindows should be used.

When an user clicks a tweet in Mauku 2.0, a dialog appears (third image in my first post). If a tweet has (known) comments or is a reply, there are options to open a new window with the whole thread of tweets related to the selected tweet (a refererred tweet with the selected comment and other comments or the selected tweet with comments). It is similar, but not the same, functionality than in old Mauku 0.x, and solves the issues listed above.

However, thank you very much for the idea. Keep them coming!

P.S. I have discussed about these things with a professional interaction designer also. Tree view was the first idea he had also. However, after some discussion, he changed his opinion.