Really, instead of three one-hundred-metre robots, why not use the resources to build one three-hundred-metre goliath (yeah yeah, didn't think it through. It would just be really skinny!) to send the monsters packing?
It might not be possible to build a robot of that size that can support its own weight, or function properly. (As noted by @MarkGabriel in the comments, see this question on the Physics Stack Exchange).
Even if it were, the weight/strength of such a robot might still not be enough to crush a kaiju.
Such a robot might also be slower, and thus not able to intercept the kaiju before they reach population centres.
And if you just build one big robot, if it gets taken down, you’ve got nothing. If you build three smaller robots, you can lose one and still have a chance of the remaining two defending you by utilising the mad skillz of the pilots.
The same reason we don't build tanks the size of buildings, or carriers the size of island chains: it was considered the most efficient cost/benefit ratio by the designers at the time. Bigger doesn't always mean better, it often means slower, heavier, more expensive and more unwieldy. Lifting a heavier arm means needing more powerful engines, which in turn make it heavier, requiring even more powerful engines, etc. The size they finally settled on must have been the one that the designers decided was the best trade-off, as with any construction project.
Also, it's worth noting that three robots of normal size don't necessarily equal one robot of three times that size: double the dimensions of a square, and you'll end up with four times the surface area. Similarly, building a 3x Jaeger might have taken the resources of 3 or 5 or 10 normal Jaegers, and at a certain point that becomes not worth it anymore.
It's actually laid out in the beginning of them film (around 2:45 - 3:15):
The Jaeger program was born. There were setbacks at first - the neural load to interface with the Jaeger proved too much for a single pilot. A 2 pilot system was implemented... left hemisphere-right hemisphere pilot control. We started winning.
Splitting control of a Jaeger two ways, apparently doable. Three ways, apparently possible, although it isn't clear to me that the third pilot of Crimson Typhoon controlled anything but the third arm, and presumably it was no coincidence that triplets were piloting it (...and that triplets are more capable of unity in the drift. In fact, I have triplets, and I can tell you that's completely untrue in real life).
How many ways can you split that control? If getting two pilots to drift together is as difficult as is implied throughout the film, then isn't three, four, five, six much harder?
This also shows up in the differences between generational Jaegers - newer ones seem to be better armed, have better materials, or have better technology, but they aren't bigger that I noticed. There's a scalability problem.
I think it's a reasonable in-universe explanation that the size of the Jaegers was limited by the ability to control them, and that that was limited by the combination of technology and human capacity to drift.
Keep in mind that initially the Kaiju were smaller than the Jaegers. They were already oversized so it would be easy to simply crush them. Bigger Kaiju came over time - thus the classification of size.
So as far as I can tell, the answer to your question is, "They did. The Kaiju got even bigger."
A) The makers did not know that Kaiju's were bound to get bigger (category n) after every event or so
B) It's difficult to implement neural load sharing among more than two pilots as it is equally difficult to find pilots that are drift compatible
C) The govt hoped Anti kaiju wall would be a viable alternative and therefore diverted funds meant for Jaeger program. So the military poured whatever's left into creating digital jaegers that are fast and effective (unaware of category 4 kaiju Leatherback)
Assuming Jaeger follow a cube-power law - that is: because they're three dimensional the mass, and thus resources, go up to the third power of height - pooling the resources from three 100m robots won't get you a 300m robot, it'll get you a 150m robot. Moreover since the robots are built in humanoid fashion you're still only getting two arms to attack with; the three 100m robots are therefore going to be able to deal three times as many blows on the Kaiju - albeit blows of lower power.
Another thing to consider is that the film explicitly calls out the early Jaeger being bigger and bulkier. Of the remaining Jaeger the bigger is also the oldest; this suggests that refinement of Jaeger design in the world as led towards smaller, faster Jaeger being a more optimal solution compared to oversized behemoths.
Finally, the real reason is none of this - let's face it, Jaeger don't make engineering sense - the reason for having smaller Jaeger is that it makes the film more enjoyable. Watching the Jaeger fight monsters as big or bigger than them is more visually engaging that watching a Mega-Jaeger crush tiny Kaiju, and having multiple Jaeger makes for a better storyline.