I think the reason why Ichika is weak is because he tried to have a peaceful life. He learned material arts from Chifuyu for self defense, he wasn't trying to be a warrior or a soldier. Houki and Rin chose their lifestyles because they believe "might makes right".
It's also possible Ichika subconsciously suppress his natural abilities because he didn't want to be seen as a monster. That's why he avoided thinking about how he could pilot a IS, he knew he didn't want to know the answer.
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