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The autotarget gets more unbearable the further into the game I get. Seriously, mission 11 is full of torpedoes, and sure the ships get better at shooting them down, but they're not perfect and a lot of them get through. The autotarget doesn't want me to help though. Instead it wants me to destroy the corvettes. I understand that the corvettes are the things shooting the torpedoes, but they're not doing much damage by themselves. I seriously have the heart to go into the game and hardcode every damn priority into torpedoes. I've been banging on my laptop a lot, and for the sake of its hard drive I really hope the developers make it a priority to do something about the targeting system.

Let me throw some ideas out there.

1. Record last targeting mode used. If it's forward targeting, record last targeted type, and always target that type, even if it's stealing the current target and putting it on something else.
2. If I'm to protect something, objective mark in order of threat (defined by damage and speed). E.g. torpedoes, bombers, beam cannons, flack cannons, then corvette/frigate/carrier. Always prioritize weapons on ships rather than the ships themselves, unless those weapons do relatively little damage.
3. Limit targeting range. I don't give a crap about anything more than 5000 out, so I don't care if the next objective is 7000 or 50000 away, especially when I've got enemies around me. If absolutely nothing is closer, then it is acceptable.
4. For autotargeting, if the next target is more than 90 degrees away, pick something else, unless there is absolutely nothing else closer. Nothing is more distracting and wasteful than spinning around 180 degrees when there's something right next to the previous target.
5. Allow customizable priority lists, in the case you guys still can't get it right. And follow it strictly.
6. Cycling between and withing types of enemies would be great.

In earlier missions the targeting system glitches weren't that critical because there weren't that many enemies. But in the levels at the end a single targeting mishap means massive losses to ships the player is trying to protect. Inconsistent targeting also means certain tactics, such as using autotargeting in Strike Mode to shoot down torpedoes become moot. It's more than 200 years into the future. You'd figure technology has advanced enough that targeting systems won't be a hindrance.