What obstacles stood in the way of realizing William Berkley's vision for Virginia?
As one historian puts it, Berkeley, the royal governor of Virginia from 1642-1677 (with a hiatus from 1652-1660 due to the English Civil War) imagined a Virginia characterized by "a diversified economy, free trade, a close-knit colonial society, and autonomy from London." Let us look at the obstacles that confronted him in implementing each part of this vision.
It was very difficult to achieve a diversified economy, because he struggled to convince the successful planters in the colony to turn to other crops than tobacco. Many of the smaller planters who might have been inclined to focus on different crops lacked the capital to do so. Also, as noted below, Berkely failed to get consistent support from London for his plans to move away from tobacco. In any case, Virginia was a tobacco colony when Berkeley arrived, and, with some exceptions, it was a tobacco colony when he left.
As for free trade, it was simply anathema to the Stuart monarchs, and Charles II kept in place most of the so-called Navigation Acts regulating trade between the colonies and England that had been established under Oliver Cromwell. War with the Dutch under Charles made things even worse.
Berkeley wanted a "close-knit" society with himself at the top, a patriarchal vision that mimicked that of the Stuarts themselves. Virginia's political leaders would be bound to him by ties of kinship and patronage, and ordinary Virginians would exercise deference toward their betters. Unfortunately, this kind of society proved difficult to replicate in Virginia, as the gravest crisis of his career, Bacon's Rebellion, demonstrated. Bacon (a cousin of the governor by marriage) led a rebellion of indentured servants and other disaffected Virginians that burned Jamestown to the ground. The causes of the conflict were complex, involving the availability of good land and relations with area Indians, but in any case it demonstrated that Virginia was far from the close-knit, organic society envisioned by Berkeley.
Finally, Virginia never achieved the kind of autonomy Berkeley hoped for. As mentioned above, Charles II would simply not allow it, and there were other powerful proprietors in some areas in Virginia that complicated things further. Indeed, one of the most serious problems he faced was that the Crown would not support his plans to diversify Virginia's economy.