Silly stuff:
I'm not complaining too much about large mode... other then it being too small. (Really I could fit 4 windowed large modes on my display without an overlap)

Seriously:
I can understand some of the complaints. Combining The favorites and command panel into one does make sense. Its rare to need to switch between them so often that is too much trouble. A nice big mini map seems like it would be essential in the next version, considering some of the features y'all have slated in the distant future.
I more or less concur with mighty darknut's diagram. And Screen notes are a great idea for one of the main panel features.