You'll find different answers from different people. I personally wish the world of linguistics and etymology to be simpler, so I just stick to the dictionary instead of inventing my own definitions and such, then give you my interpretation of them and my observations.
Indigenous is a synonym for Native. Anything that's "Native" sprang forth naturally in an area. In a sense, an indigenous religion grew and changed naturally in the area of the adherents, which always are common in ethnicity, culture or language.
Paganism is a group of indigenous religions and spiritual traditions which are historically polytheistic.
Neopaganism is a group of contemporary religions which claim roots and origins in historical paganism.
Here are some common features of these groups of religions, although there are exceptions.
A common feature among indigenous religions is the fact that they're oral traditions, rather than book traditions. Indigenous traditions may have books, writing or poetry associated or based on the religion, but the religion isn't based on the written word. Book traditions are religions which are centered around a piece of literature, such as Christianity with The Bible or Islam with the Koran. So in a sense, while Abrahamic religions are based on the literature, in Indigenous traditions, the literature is based on the religion. Steve McNallen (founder of the Asatru Folk Assembly and Advocate for Ethnic Traditions) puts it this way: "All native religions, not just Asatru, all indigenous religions spring from the cumulative experience of a [linguistic, cultural or ethnic] group [of people]". Indigenous religions are based on history and experience from, what McNallen calls, a "folk". In a sense they formed naturally.
When I say "Naturally" in the context, what I mean is that a person or group of people didn't group together and form the rules of their religion in a book and didn't hold votes or debates about what the core beliefs of the religion should be, such as the council of Nicaea with Christianity. Instead, the indigenous religions evolved and grew, and weren't designed or intentionally constructed, like many Native American spiritual paths.
Another common feature of Indigenous traditions is that they're polytheistic. You find that people who adhere to an indigenous tradition believe in many gods and goddesses. For some religions these deities are considered aspects of a central deity(called "soft" polytheism"), other times they are distinct and separate from each other, as individual as you or me ("hard" polytheism)
Indigenous religions are ancestral and animistic. They mostly have some form of ancestor worship or veneration (if not a practice that stems from ancestral veneration) and there's a belief that trees, animals and sometimes rocks have spirits. This comes from the idea that these spirits can be offended and wreak havoc on the local people if they're not honored. Animism is also a common theme in Paganism.
Neopagan religions can be polytheistic, but they tend to be what is called "soft" polytheistic and are rarely "hard" polytheistic. They also tend to focus on Nature and The Earth. Although Nature worship is a common feature of Paganism, it's not as emphasized as in Neopaganism. They can also be monotheistic.
Instead of the definition given, another one people like to give for Paganism is "any religion not being Abrahamic". It's acceptable, but of course there are exceptions.
When "grouping" religions, there is a lot of overlap. By definition, Wicca is a Neopagan religion, but can't be considered pagan or indigenous because it only has roots in historical polytheism, lacking the same beliefs as historical polytheism and didn't spring naturally or "natively" amongst an ethnic or linguistic group of people. Germanic Polytheism can be considered a pagan and an indigenous religion, but can't be considered Neopagan because it's a revival religion, and isn't a new one only claiming roots in historical Heathenry.
Other religions, such as Voodoo, are somewhat complicated to categorize. Voodoo is a Yoruba religion (a faith which has origins in the Yoruba people of West Africa) which believes in a divine, incomprehensible, distant creator who fathered a host of entities (sometimes gods and goddesses, sometimes spirits) and these entities are the go between for the practitioner and the creator. There are three variants to Voodoo: Louisiana, Haitian and West African Vodun.
Louisiana Voodoo is sparsely found to the southern USA but is more densely found in Louisiana (hence the name), especially New Orleans. It formed with the slaves brought into Louisiana slave colonies. It also has origins in multiple belief systems, primarily Native African beliefs and Roman Catholicism. They also syncretize the African spirits with Roman Catholic saints. Haitian Voodoo is very similar to the Louisiana tradition, except the linguistic patterns lean more towards Creole, it formed from the slaves imported to the Caribbean colonies and the practices vary.
West African Vodun is the "original" form of Voodoo. It believes in the same entities as the western variants, but most have "deity" status, which is lacking in American Voodoo traditions. It mostly is secluded in influence outside of the neighboring African cultural traditions. There is also, of course, linguistic variation.
So African Vodun can be considered pagan and indigenous, because it's polytheistic, ancestral and animistic, but can't be considered neopagan because it wasn't formed in the contemporary world. Haitian and Louisiana Voodoo however can be considered pagan, indigenous and neopagan. They both are somewhat polytheistic, came into being naturally from the collective experience of an ethnic group of people (being African slaves) and it was formed arguably in the contemporary world. The neopagan title only applies if you consider 1700s "contemporary", which may be the case for some scholars as they're looking as far back as 40,000 bc.
Another Example of a difficult religion to categorize is Judaism. With that said Judaism is technically an Indigenous religion because of how it [allegedly] conceptualized Monotheism and the worship of Yahweh naturally, and not with the assistance of a great meeting of founders of the new ideology. With that said, even though it's indigenous and many indigenous religions are pagan, Judaism isn't a pagan religion. This makes Judaism an exception to one of the examples above, as it's a native tradition, but it's not oral because it's centered around The Torah. It's worth noting that there's some controversial evidence suggesting that Judaism had formed in a similar fashion to Officiated Christianity.
Some can't be categorized by the given titles. Atenism, a monotheistic Egyptian religion centered around Aten, one of the sun gods in the Kemetic Pantheon, was respectfully invented by Akhenaten. Being not polytheistic, and intentionally created in ancient times, it can't be categorized in the three groups of religions. For the same reason, Buddhism and Zoroastrianism can't be categorized.
To answer your original question, all pagan religions can be considered indigenous, but not all indigenous religions can be considered pagan.
You'll find that some religions fit a title even though the practitioners claim the opposite, sometimes vehemently. Take Hinduism, although the Hindus would be insulted by being called so, they're pagan. Hinduism is polytheistic (sometimes "hard", others "soft"), indigenous and at least used to honor the ancestors regularly. Another is Christianity. Although they're Abrahamic, by all standards except their own, Christians they're polytheistic via The Holy Trinity, leaving the sister religions Judaism and Islam monotheistic. It's soft polytheism, mind you, but still polytheism. Asatruars claim to be indigenous, but the beliefs in the nine noble virtue and the six fold goal moral code make Asatru technically Neopagan. Reason being that these beliefs only have origins in the sagas, but weren't explicitly the moral code of Germanic Peoples. For the same reason, Wicca is a neopagan religion, rather than pagan.
Regarding "left handed" paths Satanists mostly consider themselves pagan, and so do Christians, Muslims and Jews, but Pagans exclude those who openly call themselves "Satanists" or anything related from the community. Laveyan Satanists, I would say, are in the same category as Buddhism in the sense that they're both philosophical religions, lacking belief in a deity. Luciferans and Theistic Satanists I would group with the Abrahamic traditions, as Satan is an Abrahamic entity, and is the central figure in most forms of Theistic Satanism. With that said, I would categorize "left handed" paths such as Rokkatru (the focal veneration being of Norse deities of death, chaos and trickery, mostly being or Jotun descent such as Fenrir, Loki, Angerboda etc.) as being pagan, so long as they don't believe that Loki is a different word for Satan or something.
It's should be well noted that, from what I understand, most adherents of Hinduism, Christianity, Asatru and Satanism would be greatly offended if they were to hear this.
Sorry for making such a long post xD I understand if you don't read all that LOL hope you found what I've said interesting.[/SIZE][/SIZE]
denominations of Wicca.