I have not seen one reason why Alba should have been picked for Sue Storm. Let's go over the reasons she's not right for the part:
1. She's not entirely white. I have nothing against Hispanics, it's just that she's not the same ethnicity as the character she's supposed to be portraying. It would have been one thing if she just didn't look like her character, but making it worse, she's supposed to be playing Chris Evans's sister. The difference in looks is enough for people to notice, even after she dyed her hair blonde.
2. She's too young. When she was in FF, Jessica Alba was 24, and could have passed for 19 or 20. Sue is supposed to be older than Johnny, but Johnny was played by Chris Evans, who despite being around the same age as Alba, could easily have played someone several years older than her.
3. It wasn't even like she was that big a star. Back in 2004 when she was picked, Alba had a short-lived TV show and a couple parts in small, non-blockbuster movies. Sure, teenagers thought she was hot, but it's not like she was an A-list name and a big draw.
And finally...
4. It's not like she even acted that well. While she wasn't horrible, I saw nothing from her work in FF that was particularly impressive. This seems to be an opinion shared by other fans, as well as critics. Given all the other factors mentioned above, I can't see why she should have been picked over any number of pretty blonde actresses in Hollywood.