Considering they were amoral (immoral?) giant robots that could transform themselves, the Decipticons should've been more effective.
Cobra was a collection of losers, sociopaths, psychopaths, warmongers and thugs...much more amusing. Though the cartoon made Cobra wanting to take over the world just because (their political philosophy was to be explained in a planned episode, but was dumped when Cobra La was greenlighted). The comic gradually took Cobra's murky motives (cool and mysterious) and made them mostly interesting in selling weapons and encourage conflict...just for greed. Aside from Cobra Commander's tiresome revenge motives, the whole damn organization became the same as Destro's M.O.. And Destro became a near-good guy, thus following the anti-hero trend that's destroyed so many great baddies. Can't kill them, they can't really win, but they are so popular...slide them over into the good camp.
But at least he never turned into a T-Rex or some shit. Winner: Cobra.