The thou/you distinction was quite well preserved until about 1590, when Shakespeare was beginning to write. It seems to have earlier been disappearing in everyday prose. We might expect to find it in the more heightened emotional atmosphere of a play; but even there, at the turn of the century, it was by no means universal. Shakespeare makes great dramatic use of the distinction, but Jonson, for example, uses it much less. Perhaps it was more a part of Shakespeare's linguistic intuition, having been brought up in Warwickshire, where thou forms were a feature of regional speech. 

Thou disappeared from Standard English completely during the first half of the seventeenth century. It remained widespread in regional dialect (and would continue so into Modern English), and continued to be used in plays as an archaism. The distinction was sufficiently alive in the popular mind for it to become an issue mid century, when the Society of Friends movement began. Quakers disapproved of the way in which singular you had become part of an etiquette of social distance, and used thou forms to everyone, believing that this better reflected the spirit of the exchanges Christ would have had with his disciples.  

Because thou forms were now rural and nonstandard, the Quaker usage offended many. The authorities, and people with high social positions or pretensions, considered it an insult to be addressed using these forms. George Fox, in his Journal, reports that he and his followers were

in danger many times of our lives, and often beaten, for using those words to some proud men, who would say, 'Thou'st "thou" me, thou ill-bred clown', as though their breeding lay in saying 'you' to a singular.

No other organization copied the practice.

The second-person pronoun system may have simplified in Standard English; but throughout the English-speaking world variant forms continued to be used.

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