Since I’m not an expert, take it with a grain of salt.
The kana following the kanji stems are called 送りがな.
http://en.wikipedia.org/wiki/Okurigana
When kanji were imported from China over a thousand years ago, they invented the okurigana to absorb the difference between the kanji-only-writings and the colloquial language which had existed before the introduction of kanji.
e.g) 李下不正冠 → 李下に冠を正さず
In the course of the development of the modern Japanese writing system, the rule of the okurigana had been modified so as not to create confusion.
e.g1) すくない 【少】
If you wrote it 少い, what the negative form “すくなくない” would be? 少くない? Doesn’t it look like just “すくない”? So it should be 少ない/少なくない, not 少い/少くない.
e.g 2) おこなう 【行】
Even if you write it 行う, everyone could read it as おこなう. Nevertheless, how about the conjugation like おこなって? …行って? …It would seem いって instead of おこなって. So, only in order to avoid the confusion, it should be 行なって.
So, even though I understand that the rule seems like chaotic to you, we native can see the “conventional rules” in the system. There might exist some grammar terms to define the rules but, unfortunately, I know nothing about them.
