Nepal is safer, cleaner, friendlier and more traditional than India.
North India especially underwent a lot of trauma given the constant wars, famines and invasions. Kathmandu in particular has remained relatively isolated. They have the old traditional Hindu culture that was largely lost in India. They don't have plastic images of Shiva, but ones of stone and wood, as they would have had a 1000 years ago all around India. The old architecture is well preserved, too. On top of that, women have greater freedom and status in Nepal. They are free to go outside unsupervised, wear whatever they like and hang out with friends, or have a boyfriend. In India you don't see that outside of metropolitan areas.
As far as cleanliness, Kathmandu trumps most of north India except maybe the Punjab (Sikh culture is quite tidy and doesn't tolerate filth, unlike elsewhere in India where all manner of faeces and rubbish are casually left in the street to rot). Kathmandu has a lot less garbage and excrement on the streets (the river is polluted unfortunately). However, around Boudha the merchants and gonpas keep the place in good order because they depend on tourists and pilgrims. They have people cleaning the main streets and stupa area daily. Also the surrounding area where Nepalis live is generally clean. They have garbage disposal services.
Most of my Buddhist friends can live happily in Kathmandu, but not India. India is continually problem after problem. I feel constantly uneasy in most of north India (Himachal Pradesh like Dharamsala and Ladakh excluded) to be honest. The angry people, poverty, filth, unreliable services, dishonest merchants, swindlers, crooked rickshaw drivers, incompetent police and general lack of decorum amongst locals (defecating in the street for instance) never lends itself to feelings of ease. You cross the land border into Nepal, though, and it all magically disappears. It is still a third world country, but with a lot less of the problems you see in India!
As far as studying Buddhism goes, Kathmandu costs more than, say, Manjushri Institute in Darjeeling or in Dharmasala, but the lifestyle is easier and Kathmandu caters to tourists, so as far as food and coffee goes you're covered.
Also the weather in Kathmandu is better. Dharamsala gets wet and quite cold in the winter. Darjeeling is so wet your books grow mouldy. Kathmandu has a monsoon season, but otherwise it is dry and warm most of the year.