Indo Aryans are clearly not indigenous to India. Mostly migrants from West border.
Even Dravidians are not indigenous to India. They too are outsiders.
The original inhabitants are Australoid, Veddoids and Negritos. The true sons of the soil. They have been living in India since their first migration out of Africa.
When Dravidians arrived, they mixed with the Australoid, Veddoids and Negritos. The modern day Dravidians are nothing but a mix of Dravidians who came from outside and the original inhabitants of Subcontinent.
When Indo-Aryans arrived, they too started mixing with Dravidians. Both culturally and genetically. Modern day Hinduism is essentially a mix of Indo-Aryan and Dravidian beleifs.
Caste system only became rigid since Sage Manu wrote the Varnashrama system. Prior to that people could jump from one caste to the other based on their qualities. There is a reason why some Brahmins look like Dalits while some look very Caucasian. The same can be said about Kshatriya/Rajput, Sudras like Jats/Gujjars/Yadavs etc...
Lord Shiva is a Dravidian God. Original Aryan Gods were Indra(Supreme), Varuna, Vayu, Mitra, Rudra etc. When Aryan culture mixed with Dravidian culture, the original Aryan Gods were relegated to being subserviant to the New Trinity of Gods (Brahma/Vishnu/Maheshwar). Lord Shiva had the same attributes of Rudra. Hence they both were combined.
Modern day Indians, no matter which caste they belong to, they all have Indo Aryan + Dravidian + Australoid/Negrito blood in them. The percentages may vary and based on those percentages, the looks might differ. The same goes for Pakistanis/Bangladeshis/Nepalese/Lankans.
Very good post . This is what most modern studies point to .
The problem with the British/european made made aryan Invasion theory is that , is considers the arrival of aryans (Ancient North Indian or ANI is the correct term) from the North west of India as on e big wave of invasion which simply pushed the Dravidians (more accepted term Ancient South Indian or ASI) downwards.
But the fact remains that the migration happened in small waves of to & fro movements. And at every stage you will find the ANI, ASI , Australoid/Negrito phenotypes mixing with each other to create the hybrid Indian races we see today.
The only pure races that you may find today in India could be the tribals who still retain the original Australoid / egrito genes as they were chased into the forests &/or were social outcasts that their genes didn't mix further with ASI or ANI.
The average South Indian non-brahmin will still have between 30-40 % ANI genes, while the South Indian Brahmins have close to 50 % ASI genes in many cases, hence the dark complexion. In north again the darker looking Indians will have a higher proportion of ASI genes (Biharis, Bengalis, etc for that matter) . SO the highest concentration of ANI can be found in the North western Indians and modern day Pakistanis, irrespective of caste, with the Brahmin and OG Kshatriya groups (not promoted Kshatriyas like in South) will have the highest ANI genes % . W.r.t the Pakistanis/Afghans, the later waves of European (Alexander) and Middle eastern invasions also played the part in the mixing of genes which lead to the super fair complexion and European features you have today.
And like [MENTION=141520]troodon[/MENTION] said, modern day Hinduism is a fusion of the Aryan and Dravidian belief systems. Obviously the Aryan brahmins who were the priestly class thus the most powerful were able to influence how the belief system was set up. Which is why modern hinduism always seems to have an vedic slant.
It is also believed that ,vedic Hinduism being a poorly defined religion , was able to integrate / appropriate the local beliefs of all the Indian lands it went to , instead of say wiping them out like with the abrahamic faiths in middle east or Europe.
So any and every god that came across as the modern religion spread , was added to the hindu pantheon either as avatars of established gods or as their sons/daughters/wives etc.
The best example for that I can find are the two patron gods of South Indians -
Murugan/Subramanyan for the Tamils and Ayyapa for the Keralites, both worshiped chiefly by Non-Brahmin, Non-Kshatriya (mostly Shudra) castes. These were the main gods of most of south Indians , and have very few temples dedicated to them outside of our states, especially in north.
Though it is said that
Ayyapa == Dharma Shasta and
Muruga == kartikeya, it is believed that these were written later to equate these gods to existing ones in the vedic pantheon.
Similarly we have lots of Tribal gods and goddesses in India, who used to be worshiped by the different marital tribes of Kerala who became the Nairs, Ezhavas, Thiyyas and the dalits.
We call them as 'kuladevatha' or 'caste - godesses' . Many of them have no place in actual vedic Hinduism. But as our communities were integrated into vedic Hinduism by the brahmins many of these gods and goddesses were appropriated as
Avatars of
Vishnu, Siva and Shakthi (devi) , while for the dalits , their gods were deemed too
lowly and hence discarded.
If you look at many of the tribal / dalit communities and certain Shudra castes (including people of my community) in our states, they still worship gods by the name of
Chathan (aka Shaitaan) , Maruthaan, which are considered
demons / asuras in Mainstream hinduism.
The closest parallel I found for this phenomenon in the west is in the abrahamic faiths, especially
Christianity . The concept/image of
satan for Christians is directly modeled on the image of various
pagan gods of the middle east which were replaced by Christianity.
My guess is that by establishing the older set of gods as demons , they could prevent the new converts as well as successive generations from rediscovering them or going back to the indigenous faiths. 
. Going further back and trying to claim some sort of purity and superiority is silly. 
