In terms of weapons the vanilla weapons the auto assault and scout are quite simular to the traditional federation and rebel weapons... in specific this is the weapon list the auto ship uses...
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<name>LASER_BURST_1</name>
<name>LASER_BURST_2_A</name>
<name>LASER_BURST_3</name>
<name>LASER_BURST_5</name>
<name>LASER_HEAVY_1</name>
<name>LASER_HEAVY_2</name>
<name>MISSILES_1</name>
<name>MISSILES_2</name>
<name>MISSILES_3</name>
<name>BEAM_1</name>
<name>BEAM_2</name>
<name>BOMB_1</name>
<name>BOMB_FIRE</name>
<name>BOMB_ION</name>
<name>ION_1</name>
<name>ION_2</name>
<name>ION_4</name>
<name>LASER_CHAINGUN</name>
<name>ION_CHARGEGUN</name>
So we can see here it uses all the burst lasers and other lasers as well as the heavies
It uses most bombs besides the breach, and it have an impressive array of ions and a few beams.
The auto ships are infamous for having 1 of each kinda weapon.
ie a bomb, missile, ion, and burst laser.
or a missile, ion ,beam, and laser. etc... So the starting load out should have 2 or 3 weapons that isn't the same type.
Drones is also common on the assault, and it can help you out... The problem with AI ships is they can't repair fires and breaches... breaches is a problem if you can't repair them you can't repair the system.
The 3 most common ways to counter this problem is...
1) have crew onboard. (Lanius, ghost, or normal crew if o2 is present)
2) slug repair gel. (if you use this, be a bit more fancy and rename it. as this isn't a slug ship)
3) drones. specifically repair drones.
Some popular ideas are having the auto ships to start with slug-like weapons, ie fire beams, anti bio beams, etc.
which I find weird as slug ships rarely have these in the modding community
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<name>LASER_BURST_1</name>
<name>LASER_BURST_2_A</name>
<name>LASER_BURST_3</name>
<name>LASER_BURST_5</name>
<name>LASER_HEAVY_1</name>
<name>LASER_HEAVY_2</name>
<name>MISSILES_1</name>
<name>MISSILES_2</name>
<name>MISSILES_3</name>
<name>MISSILES_BREACH</name>
<name>BEAM_1</name>
<name>BEAM_2</name>
<name>BOMB_1</name>
<name>SHOTGUN</name>
<name>LASER_CHAINGUN_2</name>
<name>ION_CHARGEGUN</name>
<name>ION_STUN</name>
This is the federation weapon list.
Pretty much the same but more missiles, less bombs, no ions (besides both AE ones), and the vulcan and flak.
Fed normally do burst laser + missile.