Well, he is the only know male pilot, and brother to the best IS pilot ever.
His sister, best pilot ever, is a friend to the IS creator.
IS system is totally closed and under control of said creator.

It's not hard to guess that said creator decided no males would have access to IS suits as a political/philisophical choice. It seems like the world is at peace, one could think it is thanks to the IS being controled by women. It is a well managed, overpowering force that would just stop any war in a matter of minutes. Give that to males, and the world is doomed.

So now the question is why would that creator allow for an exception, even for a friend's brother?

Regarding that guy's abilities, I guess he shares some qualities with his sister. It seems he was also at a fairly high kendo level, so knows how to handle a battle, strategy, reading the oponent and so on. I guess they want us to swallow those 2 things are enough to explain his godlike control.

Regarding the battle itself, it's as Kraco said, the match is really unbalanced in many ways:
Female Prodigy vs Male total rookie-> Female as an advantage
Fitted IS vs Standard setting-> Female as an advantage
Long range Attacks IS vs Close Combat IS-> Male as an advantage, since there's no surprise effects and no place to hide.