Yes, the Koopalings have returned. For real. They show up to battle you one at a time in Mario & Luigi: Superstar Saga! And they've got sprites that actually LOOK like their artwork now! Don't believe me? Go to your nearest game retailer and look in the strategy guides! They've got real screenshots!
BTW, the game also features a returning appearance of Chill, Fever, & Weird the Viruses (from Dr. Mario).