In the cartoons: The Deceptacons. Despite the bad writing, their motivations made sense and you understood what they were after. Each character was easily identified, most had a distinct personality with lots of power plays and backstabbing, and they just looked cooler.
In the movies: Cobra (sans the Commander). For all the same reasons above. To this day I can barely tell who's who in the Transformers movies. The sole exclusion is Soundwave who I thought they updated brilliantly. The main thing I hated about Cobra was that everyone was basically a magically-controlled -- I'm sorry, "nanite"-controlled -- slave. Villains are so much cooler when they have their own free will and motivation.