Well, this is a very sensitive issue.
Like China, Pakistan is a multi-ethnic country. Pakistan's Eastern provinces (Punjab, Sindh) share plenty of common connections with the corresponding Indian regions. Pakistan's North Western province (KPK/NWFP) has shares historical cultural connections with Afghanistan, Pakistan's South Western province shares historical connections with Iran & the historical 'Khorasan'. Pakistan's north shares common historical connections with Tibet, China; & a form of Tibetan is spoken in Pakistan's Gilgit-Baltistan province as well.
To summarize, Pakistan is a multi-ethnic country. About half of the country (Western parts) shares absolutely no connection with India, whereas the Eastern half does. The Indus river is important to understand if you want to understand the historical connections between various regions in South Asia. But yes, there is a major conflict point between Pakistan & India: India claims to be a secular state, whereas Pakistan isn't one.