Oh, prequel designs discussion! How I've longed thee! ...
Honestly, the prequels were very hit-and-miss design wise. I loved some things, I hated others. Apparently I'm in the minority for liking The Phantom Menace the most out of the three and I also believe that it had the best designs. Particularly the Naboo fighters.
Doug Chiang initially designed them with a widened tail boom to accommodate the astromech droid but Lucas revised the design as it wasn't streamlined enough. Here's Doug's original concept:
I am not sure if true but I've also read that the two renditions of the Jedi starfighters underwent a similar treatment so as to be sleeker (and the full scale AOTC prop cheaper), hence why Artoo doesn't fit inside.
I liked the blasters, the Naboo soldier uniforms, most of the Trade Federation vehicles and ships. The battle droids are not a bad design and if they weren't total idiots as characters I'm sure more people would appreciate it.
I also loved the (briefly seen) Separatist capital ships in Revenge of the Sith. I know they're based on unused Rebel cruiser designs for Return of the Jedi, which might explain why I though the fitted great with the OT design aesthetic (minus the bright coloration). Loved the Invisible Hand. Stupid name for a warship but great design. I only wish it was featured more prominently, as well as the other Separatist ships, in ... well, pretty much everything prequel related.
What bothered me was the lack of design cohesion. I didn't mind that TPM looked sleek and polished unlike the rusty OT but I hated how there wasn't an overarching design aesthetic within the prequel trilogy and within the various organizations. I would have preferred for the entire prequel trilogy to be different visually rather than "evolving" toward the OT. Which didn't even work out fine.
Say, the Separatists - why didn't they keep those awesome AAT tanks from the first movie (aside from LFL selling toys)? Instead, we got increasingly boring "tank" droid designs. Many of the existing designs deteriorated by Revenge of the Sith. Droid control ships, which became like donuts not only in shape but in their colored toppings, and the droid starfighters.
What I honestly hated were the Jedi robes. Okay, wasn't Ben Kenobi wearing just some tattered robes suitable for a desert hermit? Like pretty much everyone on Tatooine, aside from the hooded cape?
Nope, they're now the standard Jedi uniform. Which looks silly, pretentious and out of place.