In a game with the Mentak Coalition attacking the Naalu Collective, which happens first? Do the mentak fire their cruisers, or do the naalu run away? Both happen before the space battle step, but no where in the rules or the errata or faq do they address this specific situation. Are they simultaneous?

Rules-wise, I believe Corey once ruled that the defender chooses the order of pre-combat abilities. Therefore, the Naalu would get to bug out before the Mentak get their pre-combat shots. Thematically, it makes sense; I would think that the psychic abilities of the Naalu would trump the Mentak sneak attack.

Not quite. The Naalu retreat ability occurs before the Space Battle step (and after Space Mines), while the Mentak special ability is a pre-combat ability. Pre-combat abilities are part of Space Battles; they just take place before combat rounds. Archon is correct that the defender chooses the order that pre-combat abilities occur (per the FAQ), but the Naalu ability takes place before that starts.

This is important because say the Mentak are attacking with cruisers, a carrier and some fighters, and the Naalu have some destroyers and decide to retreat. If the retreat was a pre-combat ability, the Naalu could do anti-fighter barrage and kill some fighters, and then flee before the Mentak could use their pre-combat cruiser ability.

Instead, the Naalu just flee, and they can't get a bunch of extra shots in before they go. (And the Mentak still don't get to use their ability)