I think you guys are not quite getting the eastern system and the definition if what makes up a god in Shinto and Buddhist thought. I see people are constantly equating deities in Zelda to Greek myth, well that does not cover all ends at all. And I think it would be best to not use the Greek model to cover all things polytheism because different cultures have different definitions. Yes they are all immortal and all powerful to the Greeks, but the Norse gods were very different and the Celtic gods even more down to earth than that. Many did live in various areas on the land and some were almost as normal as the people they lorded over. Not everyone maintained the concept of immortality for deities either, Norse and Celtic gods died on a few occasions, as well as Persian and Babylonian gods. Also in other cultures very different things would be considered a deity and worshipped by locals for things like fertile ground or rain, etc.
Especially in Shinotism, where a large rock or especially old tree could be considered a deity and worthy or worship by the local people. Clear it is not an all powerful immortal being that encompasses a thought or concept, but it is no less a deity. Shintoism also makes a clear divide between the aristocratic gods of heaven and the more common gods of earth. While the gods of heaven might be closer to the western concept of gods that rule from on high. The lower class of gods were much more common and lived in various places on the earth and impacted people's lives more often. They were certainly not considered all powerful immortal alpha and omega beings. Many were just the residing spirit of a lake, river, or mountain. And were more like a spiritual noble lord that ruled it. Even then you have to remember that the original high creator goddess Izanami that helped form the universe, died in childbirth and remained dead after that. So even the higher gods were not all powerful either.
I also think RPGs have done a lot of tarnish people's concept of what makes up a deity. Whereas in games all gods absolutely must be more powerful than players. Well players are sometimes capable of blowing up mountains and teleporting through planes. Then gods must by nature be above lev 99 to start out and casually toss around world shattering spells like they are nothing. This is also not quite true, even in certain western mythologies. Celtic gods would occasionally get into wrestling matches with people and lose or be outdone in a contest. The Irish Hero Cuculain fought and severely wounded a goddess who took several forms to kill him. So the depictions of deities in a Zelda game are not all that different. Even Cyclos and Zephos in WW fit as gods of wind even though fans do not agree with it because they are not depicted as giants wearing togas and all powerful. However as lower deities of the earth that hold a position over one element they fit well into eastern tradition.
Even the storytelling of the Goddess fighting the demons and being hurt or defeated herself is not quite new a concept. Something like that has been told in many mythologies before. The Celtic gods continually warred with the Fomorians for centuries. With members of each side losing people in the fighting. Even the high kind of the Celtic deities was permanently mutilated in the fighting. The were also the Asura in Hindu tradition that were a group of powerful beings that constantly warred with the gods and tried to seek more power as a result. The Norse gods fought the Thursr, or frost giants, sometimes winning and sometimes losing in each battle. So the idea of an evil tribe of being that wage war with the gods and occasionally kill one or two is a time honored tradition in many different cultures around the world. Zelda is not quite unique in this aspect. So the goddess Hylia could very well be a goddess herself, just not one in the Geek mindset that is infallable. Even then the Greek Gods were afraid of and came close to being defeated on two occasions. The first time against the moster Typhon who defeated Zeus at first but was later stopped. Even then he could not be completely defeated in combat and instead was sealed underneath Mt. Etna. The other time was when the gigantes, who were described as just giants, invaded Olympus. It took the combined efforts of the gods, the fates, and Heracles to defeat them since it was prophesied that the gods would have been defeated in that battle. Even then three giants are also buried in the earth instead of killed which is described as how earthquakes are formed by their writhing underneath the soil.