I was unsure weather to post this here or on the Nova board but seeing as I couldn't get to the Nova board and the fact I think I'll get a better answer here, I posted here.
I was just messing around today with a Fed Carrier and was enjoying watching the fighter swarm AI doing its thing when I noticed something interesting. A couple days ago I had been flying an Auroran Carrier and when my Phoenixes were in a group with Firebirds they would regularly fire off their Radar Missiles and return to my bays to reload. With the Fed Carrier and its Anacondas I noticed that for the most part that wouldn't happen. The Anacondas would just follow along and attack the enemy with their light blasters only and very rarely using their IR missiles. I did find if I make the IR missiles explosion not able the hurt the player the Anacondas use them like I think they should. So I just wanted to ask people smarter than me why do they do that? What is the technical reason that Anacondas don't like to use their IR missiles?
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