What i think will be doable...
Same dimensions of case (but without all the flaws of the current)
A 5" screen (unknown resolution for now)
A better keyboard (the current is good...but i think it could be improved)
Better nubs
A new mobo with updated hardware.
I would go even simpler than that. Every new component, new hardware piece, new design costs time and money. I think we should keep whatever isn't 'broken'.
Same case - only modify if/where needed to fit the updated hardware. KISS is an understatement.
I'd love to have a 5-5.5" 720p screen in it - yes this would require the inside-lid bezel piece to be significantly modified and the speakers to move.
Use speakers with clear membranes. Wrap a split-rubber washer around them to prevent buzzing/vibrations and shove them up where the light pipes used to be - the light pipe holes become speaker grills. The lights still shine up and through too.
Keep the keyboard - the current one is not only good - it's actually pretty darn good - and good enough to not require an expensive re-design.
Keep the nubs. The nubs are excellent. Calling for 'Better Nubs' assumes it's possible to just pull them off the shelf - it isn't. The only change I would make to them is to re-case the base of them so that they ride in a socket on the MB instead of being soldered directly to it. This way if a nub is bad, swap it, test and go.
New motherboard with updated hardware is a must. If we use the current Pandora case molds as a constraint in design, and MWeston is doing the design, then all of the port positions and configurations can fall into the known column.
Starting over with a complete scratch build - that would be very expensive and would be a very long road time wise.
In My Humble Opinion Only of course - you're welcome to your opinion too.