They were founded upon religious tolerance.
Maryland was created by Lord Baltimore and aimed at being a refuge for catholics living in Britain, it was named after Henrietta Maria of France(James I's wife) whereas Pennsylvania was founded by William Penn in 1681, he was a Quaker and Pennsyvania was named after him.
Virginia was founded in 1607 and was based on agricultural exploitation whereas New England had been founded by Puritans in 1620 and was profoundly intolerant. Maryland and Pennsylvania thus became colonies with different identities.