Hole #3: Contrary to the opening narration (of course), the Tet won the war. So the clones were not used as part of its army. The Tet also orbits the Earth at some non-geostationary distance, presumably to monitor “cleanup” all over the Earth, not just around Chicago.
Now, here’s the thing I can’t figure out: Is the Tet really draining the Earth’s oceans? Or is it only draining the Earth’s fresh-water lakes? Because if the latter, that would give it a special interest in Chicago (the Great Lakes), and in the area around Lake Baikal in Russia (which actually has more fresh water in it than all the Great Lakes combined) which is on the opposite side of the planet. The Tet would not need to destroy all small-scale resistance on the planet to get its fresh water. It would just have to police the area around the lakes.
So, there might not be 50000+ clones of Jack running around all over the planet, but only a few hundred around the lakeshore, and the Tet may have made them in sequence, numbering them as they got killed, moving their houses as the edge of the lake receded.
Anyway, my point is, maybe it’s the small-scale work, the guerrilla fighting, that the Tet is bad at. Perhaps it’s not used to encountering life as complex as Man, and after unleashing mass-scale indiscriminate death from the sky, it needs squishy human brains to do the sleuthing work. Or, perhaps it’s not the human ingenuity it’s after, but the appearance of a human element. That is, perhaps it’s been using Jacks and Victorias as BAIT, to draw out the human resistance. Remember how skeptical the Scavs were about Jack’s suitability to help them at all? How many other times had they tried and failed?