So last night I volunteer to help a fleetmate test out his new Jem'Hadar carrier setup, we PvP. I don't do a lot of that, and he does, so I knew I'd get spanked, but fine I'll help him test his setup.

He's got that Tier IV New Romulus rep power that every time he criticals it has a chance to placate me for 2 seconds so I can't shoot him. Kind of a neat power on it's own but against a carrier I've never faced this before and... yikes. Every time I'd get placated, I go to hit space bar to start shooting again. And the auto targeting picks one of his carrier pets. 100% of the time. Tabbing through targets tended to hit 3 or 4 pets before I'd get to the real target I wanted too.

It wasn't pretty.

Is there a setting I can change to make auto targeting's thought process suck less, or is it one of those "you gotta click on the one you want" times?

There are a bunch of auto-target settings in the Options menu(s). There is even one for ignore pets

In the options menu, there is an option titled "Never Auto Target Pets. Enabling this option is the easiest way to deal with that problem. You might want to turn this off in PvE, or you will never be able to auto target NPC carrier pets.