The main reason was the lack of capable leadership like of Shivaji and the first three Peshwas had provided to the Marathas.
Indeed there were other dynamic and great leaders like Mahadji Scindia, Madhav Rao Peshwa, Rani Ahalyabai Holkar, Tukoji Holkar and Nana Phadnavis.
2. Military reasons:
The military weakness of the Marathas was also responsible for their defeat. The English army was trained on the European pattern and was armed with modern arms and ammunitions.
The British artillery and navy also proved to be decisive. The abandonment of the policy of guerrilla warfare by Marathas also proved fatal because it weakened the striking capacity.
In fact guerrilla warfare suited the geographical conditions of the Western Ghats and was the basis for initial success of the traditional Marathas.
3. Rivalry between Maratha chiefs:
Maratha confederacy started acting as rivals and there was a continuous power struggle amongst them.
This led to rise of mutual bitterness and jealousy amongst them and any chance of cooperation amongst them became a distant dream. They fought against each other over petty issues.
Moreover, the Maratha Confederacy was a loosely knit confederation and for the fulfilment of their objectives they resorted to mutual conspiracies.
This element of enmity amongst the Marathas increased especially after the Third Battle of Panipat.
4. Economic reasons:
The Maratha economic structure and administration lacked a sound system of economy. They did not have any set provision for the proper collection of Chauth and Sardeshmukhi and therefore the income of the State varied.
It in fact depended on the efficiency of the ruler. No doubt, such a defective system affected the vitals of their state.
Their economic system relied heavily on the use of force rather than on any definite policy.
There was hardly any reliable source that could be used in the moment of crises and an overall absence of contingency fund made things all the more worse.
5. Other reasons:
There were certain mistakes committed by the Marathas for instance, initially by taking the assistance of the Pindaris who always had intentions to loot and plunder after the end of the battle/war they relied on unreliable lot.
Moreover, the Pindaris were not even steadfastly loyal to their own leaders. They could easily ditch their allegiance to another band for money.
The Marathas failed to leave any positive impact on the vanquished, since they were usually cruel to the people of the conquered territory. The latter generally preferred to view them as villains rather than as heroes.
In fact they failed to win the confidence of any such people by undertaking public welfare activities etc.
The approach of the Marathas towards other contemporary rulers did not leave sufficient scope for any kind of cordial relations with other Princes and Nawabs of India.
Furthermore, the Marathas failed to estimate correctly the political and diplomatic strength and potential of the British and ignored their early achievements in Eastern and Northern India.
Above all they failed to seize the opportunity to strike at the enemy when they were involved in struggle, conflict and war with other powers in India and Europe.