Just as you say, most openings and defences have cons, just as they have pros, if there would be a opening or defence with only pros and no cons, everyone would be playing it.
Whether there are serious cons depends on your definition of serious, and the level of play you are at, your style and so forth. There are some serious cons for beginners to play the Sicilian, cons so huge they are most likely wasting their time. Just as the Kings gambit has some cons to it that scare most strong GM's away from it, except for occasional use as a surprise weapon.
Although most openings are named after GMs who have molded their openings to some sort of advantage, even their creators don't always play their own openings. Perhaps it's because they have counters or flaws.
For example, I find the Scandinavian defense to be very weak opening that results in my gaining more momentum. I find the Sicilian to be too complex for the amateur player to gain any sort of advantage over me, although extremely good for higher levels. I find the king's gambit to be too risky for white...
What do you think? Am I simply misunderstanding some of these great openings? Are there serious flaws to certain openings or simply counterplay?