This question makes a lot of sense and I think that any viable answer will be a stretch at best (the real answer being, of course, the more interesting/suspensive narrative).
First, the events after the invasion - as described by Malcolm - tell us that Jack #49 is somehow special. He had doubts, curiosity (that book he took), he had love for the Earth (that hidden shack of his),... We can assume, since Malcolm had to wait for him for so long, that Jack #49 is somehow special... "faulty", in a way.
Of course, it's quite unbelievable that - after thousands of clones raided the Earth - two such clones came into being (remember, it took #52 only three years to become what #49 was), but we could attribute that to the movie's need for a happy end that could easily be treated as a separate (maybe deleted) scene.
The real problem here is that Malcolm based his whole plan to fight back on a very stretched premise that such a faulty clone would appear. The Tet's mission was almost done, so he would have literally waited until the Earth's final annihilation, had Jack #49 not been "faulty".
Second, one could argue that the blind annihilation of mass proportions needed mindless "machines", while the final stages of the invasion (where #49 and #52 participated) needed some fairly level of humanity, maybe some love for the Earth (to fight the "enemy" that we, later on, learn to be the remnants of the human race), and maybe some curiosity and reasoning to be able to handle unpredictable situations and the most resilient of the resistance. This would justify the clone army being mindless killing machines, and the later techs being much more human.
One stretch here is, IMO, that the clone army was needed in the first place. Why not just drones (that proved to be quite useful even against the human guerilla; imagine what would they do while the Earth was still more densely populated), or some other - maybe more advanced - technology? We are talking about an entity capable of travelling huge distances in space, cloning life forms completely alien to it, intercept its technology and comms to mimic it later on, etc.
Another problem would be the reasoning behind the need for techs to be very much themselves, manipulated through false Sally and fake memories of the past. I see no real purpose for an astronaut to be suited for a mission on a scorched Earth any better than a thoroughly Tet-reprogrammed clone or some kind of a machine.
I have no better explanations, and these do seem weak for the reasons I've given, so I'm quite certain that the movie narrative took a higher priority here than the need for the plot to make sense.
Edit:
There is one detail that I missed (of which HBhatia's answer reminded me), which does make #49 and #52 less faulty (but still doesn't explain the bad planning on the side of Tet).
It seems that our techs, Jack(s) and Vika(s), were created quite well, but for operating in total isolation. While #49 was curious and Earth-loving, he still needed the right outside impulse, which was Julia's arrival (and him witnessing the slaughter that the drones did around the wreckage). For #52, the outside intrusion came from #49 and their brief encounter, as well as Tet being destroyed.
This, IMO, does make for a better explanation why #49 was special, although he was different - as Malcolm said - and Julia coming to him (as opposed to some other tech) is a typical movie stroke of luck (or whatever that's called).
However, why sending to an extremely hostile environment something that relies on no unexpected intrusions... well, Tet had to give humanity some chance. ;-)
