My favorite prequel ship design has to be the Venator class Star Destroyer with the nifty hatch that opens up and reveals hangars and an aircraft carrier-like landing strip:
My second favorite has to be the clone dropship
I’m also a fan of all of Naboo, Darth Maul, Coruscant, the Jedi Starfighters, the art deco-like interiors on Coruscant, the Clone Troopers (especially EPIII) and General Grievous (although I’m not much of a fan of the character)
Things I’m not a fan of: Dex’s Diner, some of the more outlandish alien designs, The super-orange look of Geonosis, the fact that all the clones are CG (effects are another story in general, but I like the designs), some of the more CG-heavy planets (Utapau I’m looking at you)