I had this one for a while now (for months).
The magical girl system is kind of worthless in the long run if you look into it, and that Kyubey is pretty dumb.
Kyubey said that the MGS was created to delay or even prevent the heat death of the universe, which is caused by the universe losing energy. The problem here is that the MGS is basically, using ducktape to fix cracks in a house which might cause it to fall apart, because the MGS only solves the problem of depleting energy and not the cause of it, which is the expansion of the universe.
Speaking of the expension of the universe, heat death isn't the only theorised end of the universe, another one is called the Big Rip, which in simple terms, the universe being ripped apart from the inside. The reason I bring this up, is because like I said before the MGS does not stop the expansion of the universe, meaning that while the presumed original end of the universe (heat death) was prevented, pouring more energy into the universe by itself wont do anything against the Big Rip.
On another note, the MGS is probably does more damage than good, considering that an entire planet being laid to waste by it doesn't concern the incubators, because it seems like they only seem to be interested in keeping their universe-zombie-virus going. But why do I call the MGS a universe-zombie-virus, you may ask, and the answer is found in Null Magical Girl, where it is revealed that if humanity isn't wiped out by witches, than they would be wiped out by the homo-magica, which is basically the MGS evolved to no longer need the incubators. In the later plot of Null Magical Girl, the homo-magica is literally described to turn the universe into a zombified/undead version of itself, while attempting to spread to other timelines and universes.
The whole homo-magica situation was probably cause by the incubator's incompitance, considering that the MGS almost got out of their hands multiple times throughout the franchise, like in Tart Magica or Magia record, and don't get me started with the Law of Cycles which basically rewrote the MGS to be "less efficient".
All of this makes me wonder, if Kyuney is just plain dumb, lazy, or just not taking their own selfproclaimed mission seriously.