I just started trying out Sublime Merge and so far I really like it! I do have one small annoyance, though: whenever I edit a file (e.g. with Sublime Text) I have to manually press CTRL+R in order for Sublime Merge to notice the changes, which I tend to forget to do.
Therefore, I would like to suggest making Sublime merge refresh automatically whenever a file is changed (or whenever the window receives focus). This could be achieved by a filesystem watcher like inotify or by simple polling. I think this would be a nice, small but simple UI improvement.