A lot of the complaints about Vaan aren't because he is a less masculine character, but rather that he is a nonentity that serves no purpose in the story. He wasn't even in the original story of XII, and it shows. He has no relation to the game's plot, while other characters, who relate to both the story and have actual connections to other characters, get left out.

People want Basch because he has a personality and could have an interesting character dynamic with Gabranth (and there are plenty of people who want Ashe for the same reasons). Vaan has no meaningful interaction with the character, and has no role in the plot that could be brought out as a focus for his role in Dissidia.

He was just a bad choice of character, and the fact that he is a whiny, scrawny, wimpy little kid is not the biggest problem people have with him.