Gaurav, the reason why Nepal is a bit disenchanted with India is because of the pseudo-secularism that our government follows against Buddhists, maintream Hindus, Sikhs specifically. Now Indians in general are liberal minded and keep quiet but Nepalis are very religious people.
Turning Nepal into a Communist-Secular state was the worst blunder that GOI aided them in. Till Nepal was a Hindu nation, all communities whether Dharmic or non-Dharmic were peacefully living. But when the external powers were given more privilege and the local Dharmic community felt threatened, tensions started rising and they rightfully blame our pseudo-secular government for this meddling. Even Manisha Koirala, Bollywood actress was irritated about what GOI has done to her country and has numerous times expressed in her interviews indirectly.
Most Nepali people love and respect common Indians as brothers and sisters since there's virtually no difference between us. But they hate our government for just reasons.
Pseudo-secularism like it is ruining India, it has taken a worse toll with rise of Communist terrorists like anything in that valley. For example India having more military and money power than Nepal means we can handle Maoist and other forms of Communist terrorism well. But Nepal isn't so financially well and has a rather terrible record for corruption; even worse than northeast in many cases. So their normal society suffers due to its fragile economy and due to our negative government's meddling.
I've been there many times and a common Nepali loves a common Indian with no differences felt (as there aren't any); it is only that they dislike our government, which even I do for very similar reasons like theirs but within our country.