That is really a good little box.
I'd recommend a few dividers inside the box, just to gather like things together....
An eggcrate like insert.... but nothing straight forward like a tic/tac/toe diagram... rather something with a few variably sized comparments.
I'd be curious to see a foto of the rear. You a bit of space behind the uno, what's that used for?
I asked, becuase I just saw a KickStarter or Indigogo campaign that featured a watch sized oscilloscope and voltmeter.
the core unit could fit in that space.... just an idea for future 'plug-in' options.
(it uses an Xmega 8bit processor its here: http://www.kickstarter.com/projects/920064946/oscilloscope-watch?ref=live
I really like the idea that someone can start prototyping without unpacking very much stuff or have primary components (ie. UNO and Breadboard) loose. Rather they can be left in place and used.