The defeat at the end of the Black and White Guardians was set up by the Azure Guardian
- It seems rather convenient that the Time-Space Visualizer was found and the 9th Doctor was able to manage all this. The Azure Guardian is the Guardian of Balance and at the end the Doctor claims this is a victory for balance. Sounds like what the Azure Guardian would do if both Guardians were threatening balance.
At the end the Black and White Guardian aren't truly destroyed.
- They are beings beyond normal time. Perhaps their more physical forms were destroyed and they instead decided to withdraw from the Universe and be more subtle. The Black Guardian thus formed the Pantheon of Discord to continue spreading chaos, the Trickster is the new leader of chaos spreading.