It's not a case of Cobra being the only enemy, more of a case of Cobra representing all of America's enemies.
The early Cobra figures had a very regal soviet look because the US was still in the cold war.
Come the late 80's and 90's, America had started making enemies with the middle east, and as a result we got figures like the Night Creepers with Sinbad-swords and Turbans.
When the Ghetto culture was peaking, we suddenly had Headman and his drug rings.
When people suddenly became hippies, CESSPOOL made an appearance!
So Cobra is the only enemy in the sense that it is all of their enemies teamed up (like some lame-o Marvel crossover set)

Nowdays though, this has completely changed. It's politicaly incorrect to have such real-world connections in a toyline, and so all the characters are just made as generic badguys.

Modern politics and conspiracies may have a large impact on my future stories, as there is just so much going on right now, it's pretty scary.