While I admittedly like the sleek aesthetic of the Naboo starfighter, so it's not an issue for me, it was Lucas who insisted in the "sleek and chrome retro visuals". Still, most of the stupid decisions for the non-functionality are again his. This is Doug Chiang's original N-1 concept:
Originally he wanted to have that "bulge" behind the cockpit precisely to accommodate the R2 unit, and to have machinery put it in place. Lucas insisted it looked ugly and decided it should be "streamlined". Seriously, watch an Ep. I making-of, I've seen it on film. Doug Chiang looked very disappointed.
From what I've read on the Ep. II Jedi starfighter, Lucas again insisted on putting an astromech droid in a ship that was not designed to house it. So, again, he's to blame.
Personally, I'm happy for this. Ep. I looked different the OT, but at the same time it too was also magical and took you to a galaxy far away. Ep. III looked bland and unispired with its copycat designs.