What are the characteristics of indirect damages (Earthquake)?

1. By all masteries that would apply (single target, ranged or melee depending on distance when triggered, etc) and final damage, plus any sublimations that increase it (ruin). Some classes also have passives that increase it.
2. It bypasses armour, still affected by resistances and block
3. None really, it's just that indirect damage spells either happen on the enemy turn letting them live longer or the spell has slightly lower damage then usual to compensate.

In the case of Earthquake specifically:
1. It is unaffected by the portal casting bonus and celestial gift bonus but otherwise it's affected any other damage bonuses, masteries etc. (actually I'm unsure about critical mastery and Effervescence. I noted an increase in damage of Earthquake when I ran Effervescence compared to when I didn't run it, but I can't explain why that is so because it definitely doesn't consume the Effervescence proc. )
2. It does ignore armor, still mitigated by block and resistances
3. No noticeable disadvantages...unless you forget you're a melee build and cast exaltation outside of melee range and your earthquake does no damage.