The first AE2 quest (appropriately titled Applied Energistics 2) says:

To get started with AE2, you will need to mine an important resource for the mod known as Certus Quartz. Just like for Amethyst, you will find Certus Quartz Crystals that you can mine for Certus Quartz Dust and Crystals.

This, to me, implies that Certus Quartz Crystals are found underground in big hollow spherical structures like Amethysts.

This is not true. Certus Quartz Crystals are found in meteorites that require a Meteorite Compass to find. The Meteorites are mostly filled in except for the small area where the Budding Certus Quartz is found.

As per the AE2 Wiki:

• Put a Vanilla compass in the charger and charge it to craft a Meteorite Compass.
• Use the meteorite compass to find meteorites, which have a chance to contain quartz blocks and budding quartz.

The solution to this is pretty obvious. Either add a Meteorite Compass to the first quest and amend the description, or add a new first quest with only the compass and have the current quest become the follow up quest.

Just put in a fix for this!