First of all...first post! =P
That said, it seems there are 2 different types of complaints regarding the plot of the new movie:
A) JJ is just being lazy re-using Khan.
B) People dont like the way the Khan story is told, for varying reasons.
To the second group, you have a valid opinion which I wont argue with. However this opinion is no different than not liking the plot of the first movie. Its just a problem with the storytelling.
To the first group, I will say that perhaps the 2nd movie was too soon to use the character Khan. However I would like to make the point that the character of Khan still existed even in this alternate timeline even if he wasnt the focus of the 2nd movie. He was still floating out there in the Botany Bay, and some ship was still going to find him. Thats just a fact.
So while the 2nd movie may have been a little too soon *feeling* to use that character, the fact is that character was in this timeline and was going to be found, so this particular story is just the way it turned out. If a few more movies are made, perhaps it will feel better to place this particular story later on in the series of movies and substitute the 2nd spot for some later story. But either way, Khan was coming eventually.