I am not trying to answer this question in a comprehensive way, but must make the obligatory "Historians cant explain why something didn't happen" comment. We can't answer why India didn't get converted in totality because that doesn't fall into the sphere of a Historians work, because it would necessarily involve some intense speculation that literally cant be sourced by anything.
That being said, to stimulate some discussion I can highlight a few key points that are very relevant to the question you are asking:
We can answer why certain states did become at least plurality Islamic ie. Sindh, Punjab, Bengal. Maybe comparing these places with other regions in which Islam failed to root itself in such totality would yield some insight?
In comparing the other places Islam and Christianity have spread, you will find that not one of those places is a parallel in terms of demographic dynamics to the subcontinent. For example, India today has a larger population than the entire continent of Africa and more than the entire Middle East as well. Now while this ratio might not hold up 1:1 historically, India has historically been much more populated than either of these regions. So trying to find an explanation to India's non-conversion in terms of how other places have converted in totality is a doomed exercise. Rather, we have to approach the history of India on its own terms.
In general, Islam has obtained 'total conversion' in places only through hegemonic control of the region. Either through foreign conquest or via converted local leadership. So in that regard, you'll notice that such a climate of Islamic hegemony in the sub-continent didn't even begin til Arab civilization had already risen and fallen. For example, by the time the Delhi sultanate had even been established somewhere like Egypt has already been under Islamic hegemony for over 500 years.
The Islamic hegemony that did exist was shorter lived than in most places where Islam has taken such a dominant foothold. The Delhi Sultanate was established in the 13th century, the British declared the Indian Raj and Victoria her Empress in the middle of the 19th.
Going back to the point about approaching India on its own terms, historically it was not ever one political unit but rather a region of many various cultures and national identities. Even previous empires that had united the whole of India had done so on those terms. The sub-continent historically was more akin to the whole of Europe or Sinitic civilization rather than some consolidated entity.
No Islamic state has ever encompassed the whole of India. Alamgir the 'world seizer' came very close, but that period was also very short lived. Before and after that, this massive and pluralistic sub continent had been ruled by varying powers in varying degrees. Most of the history of the Delhi Sultans and Mughals was one of competition with other Muslim states and obviously Hindu principalities for control of the region. So basically, there was never a time that the Muslims had the entire sub continent under lock in such a way that no native Indian power had any presence. As opposed to, say, Persia which was conquered in totality.
Even when Muslims did conquer entire swathes of territory in India, they heavily relied on Indian/Hindu bureaucrats and princes to run their states. Several polities, the Rajputs of Rajasthan being a prime example, were mostly ruled under suzerainty and therefore local leaders still had a strong presence throughout.
Muslim rule in India was much more syncretic in nature (for the most part) than Muslim rule in other places. William Dalrymple writes in his essay "The Most Magnificent Muslims"
But if the Mughals represented Islamic rule at its most magnificent, they also defined Islam at its most open-minded, tolerant, and syncretic. Unlike the Ottomans or the Safavids, who ruled largely Muslim polities, the Mughal Empire was effectively built in partnership with India’s Hindu majority, and succeeded as much through diplomacy as by brute force: Akbar in particular was a true humanist who strove for the reconciliation of his Hindu and Muslim subjects, and managed to unite them in the service of a coherent multireligious state.
These are off the top of my head some very very important points that I hope will shed some context on the question you are asking. I am generally just thinking out loud here and not sourcing from any one particular place, but a couple sources that I have gathered my knowledge of Islam in India from are the following:
The New Cambridge History of India by John Richards
The Delhi Sultanate: A Political and Military History by Peter Jackson (not the director)
The Empire of the Great Mughals: History, Art and Culture by Annemarie Schimmel
The Rise of Islam and the Bengal Frontier by Richard Eaton which you can read online here
The Mughal Empire from Babur to Aurangzeb by S.M. Jaffar which you can read here
We need to immediately address the very loaded nature of your question, /u/TheCommissarGeneral, before going any further.
Most other faiths were crushed or eradicated.
Christianity is alive and well today, and has the most declared adherents of any world religion including Islam. Various denominations of what we might umbrella-term "Christianity" were the most common faiths of the Middle East at the time of the Arab-Islamic conquests, and remained so for at least two centuries after the establishment of the first Islamic state. This isn't to mention Jewish minorities which, while experiencing a long history of persecution in the region before the rise of Islam, were present and still survive today. While they became minorities and many of these communities have dwindled away or moved elsewhere, "crushed or eradicated" are terms that have extremely negative connotations and should be avoided. During the early Islamic period we see the near-disappearance of some religious groups like the Zoroastrians, for instance, but Zoroastrianism was dwindling well before the arrival of Islam, and for a variety of reasons: the marginalization of fire temples, the growth and popularity of Christianity, and so on.
The process of a community's conversion is very, very rarely at the tip of the spear as opposed to some other means. Many historians of religion/sociologists of religion would stress the huge variety of form this conversion can take place in. While it isn't unheard of to hear of violent or forced conversions taking place, very often there are a number of factors at work in this conversion, like a ruler's decision to convert and to declare a new "official faith" for a region and people; a community's elite choosing to adopt the trappings of a new religion in order to maintain their privileged status; or even an individual's genuine and passionate conversion to a new religion that inspires his family and his community to look harder at that faith than they had previously considered.
In short, while I am not offering a direct answer to your question, it's because the realities of the Middle East over the last 1500 years demonstrate that this process wasn't immediate, nor absolute. Using terms like "crushed" and "eradicated" are deeply problematic, and show a fundamental misunderstanding of the process of religious change that has occurred throughout history. While it may seem like semantics for me to write all this just about your word choice, it's because I hope it will help you to digest answers like that of /u/Cyrus47 and the sources we will provide you. Words are powerful and have great meaning, and should always be wielded wisely.
Your question starts with a bit of a false premise, at least as far as Islam is concerned. The spread of Islam did not involve the eradication of other religious groups. There weren't events like the Massacre of Verden (when Charlemagne killed 4,500 Saxons for refusing to convert to Christianity). Conversion to Islam was slow and uneven and, more often than not, discouraged by the caliphate. There are a number of reasons for this.
In the early centuries of Islam, the Arab-Muslim ruling class of the early caliphate was an extreme minority (maybe 10% of the population of the empire) and they wanted to maintain an elite status by preserving the Arab nature of Islam.
You could tax non-Muslims at a higher rate than you could Muslims and those tax revenues were necessary to maintain the empire.
Attempts at forcible conversion would have met with fierce resistance and the Arab-Muslims were just not numerous enough to put garrisons in every town they conquered and maintain order.
For more on the Arab-Muslim conquests and the relationship between Islam and other religions in early Islamic history, see Hoyland, In God's Path and Donner, Muhammad and the Believers.
The spread of Islam to India came much later (the systematic conquest of India by the Ghurids didn't start until the 12th century) and some aspects of this pattern had changed. There was no functioning caliphate left to direct the conquests, for example, so instead India is conquered by waves of Turkic and Afghan dynasties who are also competing with each other. This creates an equally uneven approach to the conquest with some rulers destroying Hindu and Buddhist religious sites while others worked to integrate themselves with the Hindu ruling classes. Large scale conversion (or, more appropriately, demographic shifts) in India probably didn't happen until the Mongol invasions when Muslim refugees fled south.
This sparked a similar question for me that might be related. I listend to Dan Carlin's series on the Mongols, and it sounded like the Mongols swept like a wave across Asia, into the Middle East, and almost took Europe as well. In all of this, what caused them to also pass up India? Were there significant geographic barriers that prevented this conquest as well as the spread of religion?