Nehru, Patel, Menon all were worried about the future of princely states but Sardar Patel and VP Menon worked on it. The Muslim League always saw princely states joining India creating a stronger India and thus creating more challenges for Pakistan and they also tried to get hold on many Hindu majority princely states. Read this Pakistani site what were they upto with princely states even trying to get Hindu majority princely states deep inside India and usual grumbling how India spoiled it.
Quaid-iAzam, Muslim League and the Accession of Princely States
You are wrong, Pakistanis believe India-Pakistan enmity started with the war between Raja Dahir and Muhammad Bin Qasim and sometime even taking it back to demonizing Chanakya in Pakistan since he is considered as a hero by Indians. Kashmir or any other territory even if they not existed, Pakistan would have still considered India as an enemy. Its about ideology , not Kashmir.