I completely disagree. First, regarding size, the 909 is as big as it is because of the component count, and the thru-hole style of circuit board. Have a look at the pics at http://hackaday.com/...r-909-teardown/ which pretty clearly show why the machine is so big.
As for the grouping of the controls: I have used the 909 extensively, on stage (live programming on-the-fly) and in the studio. I find the spacing of the controls to be very comfortable (most mixing boards are more cramped than the 909), while the extra "white space" at the top of the machine is a great place to rest another small device, or my headphones, or my glasses. And it looks so BITCHIN!
IMHO The TR-909 has a tasteful, minimalist look that doesn't detract from its usability.
My point was, either use that space or get rid of it. Putting a big blank space up top just to make it look like a real 909 makes no sense if the pcb's don't require the extra space. Just make the box smaller if you don't want to space out the interface. That'll be cool in its own way.
I think the knobs are cramped, see Jomox for proper knob spacing. Agree that it looks cool. I think a properly-spaced design could also look cool, depends on the artwork.