What were the biggest issues facing England during Queen Elizabeth I’s reign?

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Queen Elizabeth I inherited several issues from the reign of her predecessor, Queen Mary I, including an unpopular war with France and the religious divisions that Mary’s campaign against Protestantism had left behind.
The threat posed by the former subsided with the 1562 outbreak of the War of Religion in France, and Elizabeth responded to the latter by returning England to Protestantism and having Parliament formalize certain aspects of the Church of England’s doctrine.
An issue that troubled her reign for its entirety was her lack of a husband and heir, a situation which she and others realized could potentially ignite a successional crisis upon her death. Still, she never married, perhaps because she preferred to keep power to herself.
One of her biggest trials—at least in the foreign policy realm—came when Spain tried to invade England in 1588. The ensuing naval battle would go down as one of the most famous ones ever and ended with England’s defeat of the Spanish Armada, which had until then been supposed invincible.