Yeah, AP is just quite unbalanced in certain regards.
Namely, there's a few overpowered weapon skills in there (assault rifles) and some weapons are just WAY under-powered (pistols).
That Mark-and-Execute skill is way overpowered, as well.
AP also likes to use dice-rolls for hit & miss, as well - which should be a "No-no" in a game that has shooter-style controls; especially in games released after Mass Effect 2.
This shouldn't stop you from playing AP. AP has some great characters (such as Steven Heck); and the game is absolutely fantastic w/ making your choices matter to change the way the game actually plays out and its actual final outcome.
Except while the pistol is terrible when used normally, the Chain Shot skill (probably what you mean by the mark and execute) is without question the strongest thing in the game, and will kill any enemy in one go when maxed out, including the final boss. Maybe that took two chain shots. I just remember it being totally trivial.
Stealth is overpowered, with the extreme exception that it's useless against bosses.
The whole thing is sort of a buggy mess, but the story and the way choices are laid out is super cool. Would definitely recommend it for 3 bucks.