I think the highlights of India are spread around the country, and it depends on what you are looking for.
My favorite places:
Best historical or "tourist" towns: Hampi, Bundi, Jaisalmer, Pushkar, Orchha, Cochin
Best major cities: Mumbai and Kolkatta
Places that I just loved being in: Varanasi, Ladahk, Goan beaches, Kerelan backwaters, and Sikkim.