Why is it that females can pilot IS and males cannot? Is there a special reason? Also, why is it that Ichika can pilot IS?
Why only female can pilot IS ?
The reason why only females can activate the IS (and why Ichika Orimura is the only male who can do the same) is currently unknown. But it is hinted in the novel that Tabane Shinonono, the creator of IS, did not deliberately configure IS to be a female-only platform. She mentions that it was a accidental side-effect, and since she didn't really care about that factor, she didn't see any reason to bother with it.
Why Ichika is the only male IS pilot ?
A speculation on why Ichika can pilot IS.
This is my theory behind it, I think the reason why Ichika can pilot IS is due to Tabane pulling strings at the back. One possbility is that Ichika is not related to Chifuyu, and like Adam Jensen from Deus Ex Human Revolution along with JC Denton of Deus Ex, is genetically altered. This truth is possibly known to Chifuyu, Madoka and maybe Tabane only.
For those who never played the game. In Human Revolution, mechanical augmentations require the user to use a drug for life to prevent gilial tissue build up in order to use the augmentation. Adam was genetically altered (unknown to himself) by White Helix resulting his body would not form any gilial tissue. This is a secret only David Serif and his girlfriend Megan knows about. And it plays a big plot in the game as well.
Do you guys see the link here now? You might ask who altered Ichika? My guess, is Phantom Task.
If this is true, it might serve as a massive plot point considering how many leaders of the world would want to bio mod their soldiers to wear IS.