So every time I aim my rifle at someone I get a red 3% and can't hit shit.
If you're using UFO Extender accuracy option - your shots lose accuracy with distance, with auto being the most affected, snap is less and aimed the least (or not affected at all). For long distances, auto isn't that useful in that case.
Holding control gives me a gold number.
That's strange. Could you provide screenshot or video, or maybe savefile and instruction how to replicate? If there's a visibility - there should be non-zero chance-to-hit number on targeting, and if you press Ctrl - it should show you how much the target is exposed (100% for fully exposed). If target has good cover, low visibility number shows in red. I have no idea how visible target could give gold numbers with Ctrl.
When I have heavy plasma, is that 3% just my chance to hit through cover, but my plasma will take out the cover on first shot and it gets easier?
Yes, especially for "realistic" spread - first shot have good chances to destroy a target, and then consequent shots will have better chances to hit the target. You could see them in log if you enable showing rolls.
Obv my rifle doesn't do shit to cover, and aimed shot doesn't seem to be helping.
If you're using 100% cover effect you should use all you can to improve your aim - soldiers with high accuracy, aimed shots and kneeling
I'm thinking prelaser I go in with as many autocannons as possible and light these guys in cover up
Is there something I'm missing or do I have right idea?
I don't know)) You should experiment)) It seems that "realistic" spread combined with HE autocannons could beat the shit out of those pesky aliens, but I didn't tested that for all settings combinations