Is Mughal history a dominant part of our syllabus only because not much is known about the empires before that, or is it because of the political and cultural ideology of our first leaders?

On the contrary, there's been spectacularly little “research” per se done on the Mughal Empire.

Most of what we “know” about the Mughal Empire primarily comes from the records of Mughal Emperors/ officials themselves and that of contemporary European visitors to the Continent. Almost nothing regarding the actual socio-economic system of the time, the technological or economic situation, the records of contemporary Hindu powers, the actual Bureacratic and Administrative details, etc etc has been either studied or had an iota of focus laid upon them.

Habib & Moosvi, especially the latter, have -kind-of- worked on the “real” research but it's the same thing with them as well.

Why so?

See- the basic truth is that the educated classes of Endia don't exactly care for the Mughals or their Empire or their accomplishments per se, as much as they appreciate how convenient a tool they are to bash Hindus with. I've earlier answered a question on Quora regarding the technological developments during Mughal rule; they were no Medicis or Industrial England, but Mughal-era Officers were fairly into new developments and sciences.

The Mughal urbanization rate was 15% and climbing daily. The Middle Class was strengthened. There were karkhanas larger than any factory in Europe. We hear a lot about Ming and Qing bureacracy but the Mughal bureacracy arguably wiped the floor with them, dubious “meritocracy” be damned; in no other country in the World was the Government in a state of low key war with its citizens half the time and yet maintaining a fairly robust Administration.

Agricultural yield was growing daily, education was becoming commonplace, and a overall flowering of the economy was only being prevented by the usurious Mughal taxes. A key reason for the sudden growth during Maratha times- the widespread construction of temples, forts, and trade networks- is that the superstructure had already been built and the Marathas weren't robber barons like the post-Akbar Mughals were, to have wasted it.

That's why stuff like Madison's is so irritating. Mughal India was a robber baron Economy, yes, but it wasn't a subsistence economy by any means. Even contemporary observers made wild nonsensical claims with no backing. Bernier claimed that Aurangzeb was so awed with European powers that he'd admonish his teachers for not telling him more about them; such behaviour would've not only been completely out of character, it's mere expression invites the question of how Bernier got into the inner Palace Chambers in the first place. Tavernier criticizes the Mughals for not paying attention to modern military developments in Europe and claims they could be easily defeated by a European force a few thousand strong. Again incorrect- barring their willful blindness on the matter of Amrika, the Mughals obsessively followed the situation wrt the Ottomans in Europe. We even have records where they're remarking how Turkish and Firang accounts never matches. Mughal observers did visit Europe, there was discussion on how warfare worked there- including a point I recall where some Mughal officer compared Gustav Adolf's integration of light artillery into infantry cohorts to the similar style of using swivel guns in India. Of course, a hundred years later when Indian and Western powers did start clashing, almost all the initial conflicts until the mid 18tg Century were handily won by Indians.

The same pattern crops up again and again. Indian shipbuilders were allegedly useless but it turns out even European trading companies were having their Ships of the Line built at Surat by Jain builders. Indian factories apparently didn't exist but even as late as the Napoleonic Wars, even 2nd string Indian powers can churn out thousands of rockets within a matter of weeks, if not days.

The Mughals, as I've reminded people again and again, were monstrous and hold no little part of the blame for the troubles India faced later. However they were also great in their own right- surely a concept even Hari Puttar-reading Quorans can understand.

The consistent marginalization of Mughal history, coupled with the consistent tomtoming of their alleged secular virtues- virtues whose non-existence the Mughals themselves were at pains to point at through their deeds and writings- are the result of the same moving spirit within the Endian Educated Classes that leads them to downplaying the grandeur of the Gupta Empire as well as questioning the very existence of icons such as the Emperor Vikrama.

Denial of Hinduness itself.

Hinduness plays out not only in its defiance of Peace, but also in denial of the Krischan “Modern” world- a trait it shares, interestingly enough, with the forces of Peace. As such, it is necessary for the Educated classes that the latter's natural antipathy for the pagan be played up, not only to assist the Powers-that-be to wipe out the Hindu weltanschauung but also to enforce their “domination” over the Peaceful and the Peaceful's over us.

That's what it is about, at its core.

As for the bandit Jabberlal Neckscrew, what words remain to be said? As the glorious leader himself remarked while receiving the Balut Raita, quoting Ranbir from Padmavaat: “Yeh Taufa humne khud Ko diya hai.”