Louis Wu says this article is supposed to have three parts, so I guess this is the end. Weapons? Covered. Characters? Covered. NPC behaviors? Covered. Cover? Covered. What's left? Oh, right. Story.
Plot Holes You Could Drive A Warthog Through
Normally, when one is talking about plot holes, one is referring to elements of a work of fiction that cause the audience to lose suspension of disbelief: characters acting contrary to their nature, unlikely and unexpected events, strange conspiracies of circumstance and coincidence. Things that make you want to lean over to your neighbor and say, "that would never happen in real life".
Works of fiction in fantasy and science fiction universes have a lot of different ways to conceal those flaws: magical mysteries and high-tech mumbo jumbo. Wizards are people who can summon fireballs from thin air, and the Enterprise is a ship which, by very definition, travels faster than the speed of light. All that remains is for these fictional universes to remain self-consistent. Which they sometimes do.
Gears of War, though, has some plot holes. They're different kinds of holes. Most of the time, characters in Gears are fairly easy to understand, and act in accordance with our expectations. Since most of the time we expect them to be either kicking ass or taking names, we are not confounded when these things occur. So when something happens that does seem unexplained, it stands out. Some sharp readers already pointed out a few, but I'll try and start from the beginning.