I believe the Koume and Kotake of Termina are different from the ones seen in Hyrule mostly because of the conditions that created them. Termina has a very different set of circumstances that could have created a more villainous character
Ganondorf gave us some information on his motivations in Wind Waker
My country lay within a vast desert. When the sun rose into the sky, a burning wind punished my lands, searing the world. And when the moon climbed into the dark of night, a frigid gale pierced our homes. No matter when it came, the wind carried the same thing... Death. But the winds that blew across the green fields of Hyrule brought something other than suffering and ruin. I coveted that wind, I suppose." — Ganon
The Gerudo of Hyrule lived in a much harsher region that, as Ganondof said, "brought suffering and ruin." So that anyone growing up in such a place would be much more accustomed to death and suffering, and would be a more hardened individual because of it. While also they lived near the very prosperous Hyrule with all the wealth and plenty that they coveted. This would undoubtedly cause tension between the tribes as the Hylians lived free of the harsh conditions of the desert in peace and prosperity. This coveting probably turned to hatred over time. The Koume and Kotake of Hyrule would be no exceptions to this as they lived for 400 years in these conditions.
Another factor is the presence of Ganondorf, who we learn from a gossip stone that the Gerudo worship like a god.
They say that Gerudos worship Ganondorf almost like a god." — Gossip Stone
Nabooru also stated that she was disgusted by the evil and cruelty of Ganondorf, which very likely had a corrupting effect on the Gerudo people since they were said to worship him like a god. They were inclined to follow his direction since he was both their ruler and possible deity bringing the Gerudo towards evil. Instead of just thievery, they were loosing any honor they once had.
First of all, let me introduce myself. I'm Nabooru of the Gerudo. I'm a lone wolf thief. But don't get me wrong! Though we're both thieves, I'm completely different from Ganondorf. With his followers, he stole from women and children, and he even killed people! A kid like you may not know this, but the Gerudo race consists only of women. Only one man is born every hundred years... Even though our laws say that lone male Gerudo must become King of the Gerudo, I'll never bow to such an evil man! By the way, what is your name, kid? Link?! What kind of name is that? Well...anyway..." — Nabooru
Slightly before the events of OoT there was a war between the tribes that the Gerudo apparently lost. As Ganondorf was first seen in Hyrule Castle swearing loyalty to the Hylian king. So loosing a war to the very people they resented would cause the Gerudo to have even more animosity. The anger and embarrassment of their own leader and god actually having to bow in defeat and swear loyalty to a foreign king might have been too much to bear. Especially to the surrogate mothers of the very man who lost and had to bow before the Hylian king. This would further move them towards evil.
Now in Termina the conditions are completely different. The Gerudo do not live in any desert at all. So there is no frigid gale or searing wind to cause suffering to their people in their daily lives. Nor is there a larger and more prosperous kingdom nearby for them to covet. And no wars were fought causing them to swear loyalty to any foreign rulers. There is no religion of the triforce to create aggression between the tribes. And there is no Ganondorf present to worship and be corrupted by with his excessive evil and cruelty.
The Gerudo of Termina were simply thieves, they did not have any country conquering ambitions or plans to steal any eternal symbols of the gods. The younger and more adventurous Gerudo became pirates while the older and less bold Koume and Kotake were content enough to make money selling potions to the people of Clocktown. They were probably beyond the age of robbing travelers and merchants and settled down to make potions. Without Ganondorf or Hyrule kingdom, they have no need to be evil, no one to hate, and no villain to follow.
