Does empire region or the NPC agent determine which pirate faction you will be fighting against the most when doing secuity missons? Basicly I want to start using T2 projectile ammo in auto cannons so would I be better off choosing a Minmatar agent or stay in a Minmatar region? T2 projectile ammo has only kinetic and explosive bonuses, not very useful if a secuity agents give me alot of missions fighting against Sansha, Blood or Mercs. Maybe T1 ammo would be better because of the different damage types they offer.
It is predominantly based on the region the agent is in.
https://wiki.eveuniversity.org/Projectile_ammunition
T2 ammo wouldn’t really give any reasonable benefit. Stay with faction ammo and chose for resist holes.
For best income it would be way more beneficial to focus on agent with best isk/LP conversion in system that pays the best (lowest truesec). Income from extra LP efficiency would be higher than locking yourself to potential low isk/lp conversion and lower pay per mission.
But to answer your question. Yes, region of space you take missions in. Determines which rats faction you will mostly fight against.
Open up the standings of that agent’s corp the greatest enemies (with the highest negative) is what you will be fighting most often.
https://www.fuzzwork.co.uk/lpstore/
Is your friend 
abuse it well.
If you like auto cannon’s then you have a lot of options:
Republic Fleet Phasted Plasma: Gurista’s/Serp/Caldari/Gallente/Mordus (But mini have low sensor str so you will be jammed alot by guristas) Serp hit into your resist profile holes for t2 mini resist profiles (kin/therm) so its possible but not optimal.
Republic Fleet EMP: Blood Raider (Super low tank’s / EM damage / Neut’s) if you use a Vargur which I’m Guessing is the direction you are heading then blood raider is probably the easiest enemy as you have nos potential from extra high slot’s you will melt them super fast and tank them super hard.
Sansha/Amarr/Khanid - Ignore the damn tracking disruptors will be a nightmare for you.
Hail/Barrage/Fussion - I’m guessing this is what you want the most.
Best would be Angel/Minimatar
If you want to be in high sec then yea I would join a minimatar agent but if you want more isk/hour maybe try go to lowsec and join a corp that hates minimatar.
For reference bounty on angel rat’s highest gets to around 2mil, but if you fighting minimatar ships they can drop a tag worth 5mil, so that alone is 2.5% more isk/h but being in low sec will increase the lp gains as-well.
If you want to kill Angel
I would suggest joining Servent Sisters of Eve they hate Angel at -7 and have higher lp than Minimatar.
https://www.fuzzwork.co.uk/lpstore/sell/10000002/1000130
If you want to kill Mini (Highest isk/h in low sec for your play style)
Then Amarr/Amatar (Low Sec)
Angel/Syndicate/Serp (NPC Null sec)
Also one last thing don’t worry to much as you can decline a ton of missions if you get your social skill to V your biology to 4 or 5, your faction standings up high and you buy this thing:
Then you can cherry pick only the ones you enjoy the most.
I just used T2 Large Hail in a Vargur with level 5 skills on everything. Activate Bastion mode and Hail doesn’t care what your resistant bonuses are. Ships start exploding in about 4 to 6 seconds. Thanks for all your advice on different pirate factions. I figured its just easier to hit em with Hail / Barrage and scrape up the salvage with a mobile tractor. I can see why T2 Autocannon Projectile sell so well. I went to Jita last night and bought over a 250k shells. That should last awhile.
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