Well with StackOverflow they are using tags, they tag topics, not categories... Our case is different x/ we aren't tagging topics, we want a main category let say call it "Anime" with an alphabet A-Z sorting for the sub categories and each sub-category has its own topics.
Sub - category represent each anime title
http://myanimelist.net/forum/?subboard=1
Would this be the same issue if i tried this with XF? i know XF is light. And since it is using Zend framework, we are familiar with it. I am hesitant to buy XF just to face the same issue, also the company's bullying manners which i disliked very much.