While I agree with what you're saying, I would argue that many of the ways that currently exist in the game to get through fireballs are kinda crappy, and therefore are only really effective if the fireballs themselves are crappy. See, for example, how Charlie can use his V-Skill to absorb a fireball, but the startup and recovery on it are so long that characters with good fireballs (like Charlie himself, or Guile) can quickly close the distance on him and punish him. Or how Cammy can easily V-Skill her way through Ryu's fireball and punish him, but has a harder time doing it to Guile (and at times it can even get her punished instead). There are also many good moves that get you through fireballs (fast moves that have armor or projectile invincibility, etc.), but those often require the use of an EX bar, and in a game where you can only have three bars at most you won't always be able to rely on them.
So I feel like the issue can be kind of complicated.