Your comments

A branch is not part of a commit in Git, but just a named pointer to a commit. The colors are just that - colors for making the log easier to read - they don't refer to any specific branch.

I don't understand the argument "especially if you work in a team that uses a lot of feature branches and Pull Requests". Could you please describe your work-flow?

Fixed since 17.1 preview 4.

Just select both commits (where the branches point to) in the Log and you will see the diff in the Files view.

Do I understand you correctly, that you want to add the same repository (= directory) to different repository groups? That won't be possible because we maintain a set of directories.

With SmartGit 17.1 preview 3 it becomes easier to create own themes: http://www.syntevo.com/blog/?p=4391.

Please distinguish between 2 windows and 2 instances. If 2 instances of SmartGit are running (with the same settings directory), this is a bug. But 2 or more windows is by-design.