In the light of a few runs that has been rather tricky due to issues with targeting abilities, I was going to suggest a way to lock your targeting to a set amount of targets. Maybe use the awesome small windows in the right corner, and use something like L + click and then those target boxes you click will have a red outline around them, which means when you cycle through ships with a set key, only those targets will be chosen.

This would improve things greatly. I have always wanted a "cycle through hostile targets" key. I've also got to say that the current code has messed a lot of things up since it's no longer possible to do a true cycle of all targets with the constant resetting.

One (or multiple) focus targets similar to what WoW and other mmorpgs offer would be nice to have. I agree

Mini-icons in the upper left for every hostile target to you would be really nice.

In principle yes, but this could get super cluttered in PvB and when slaves and drones are involved. The current thumbnails for friendly squad+slaves+drone is already pretty cluttered and hard to manage.