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.
scifi.stackexchange.com/users/440/Paul D. Waite
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.
scifi.stackexchange.com/users/20221/Nerrolken
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.
scifi.stackexchange.com/users/20490/gowenfawr
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."
scifi.stackexchange.com/users/406/Adam Davis
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)
scifi.stackexchange.com/users/35407/chiru
This is an engineering problem.
Let's say it takes x amount of force for a Jeager of average size to move its leg y distance in order to walk.
Using proportions, it would take a Jeager 3 times average size & weight 3x in order to move y/2
scifi.stackexchange.com/users/43103/Kings Adviser 
Probably same reason why the opposing side did not grow even larger Kaijus to crush all Jaegers easily: there are limits on how large the things could be.
scifi.stackexchange.com/users/25835/h22
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?
Why didn't they build the Jaegers twice as big as the Kaiju to crush them easily?
scifi.stackexchange.com
<pacific-rim>
scifi.stackexchange.com/questions/71483
scifi.stackexchange.com/users/35371/Finnball
With three smaller robots, you can lose one and still have a chance of the remaining two defending you. Also, bigger doesn't always mean better - it can means slower, heavier, more expensive and more unwieldy. Lifting a heavier arm requires more powerful engines, which in turn make it heavier. An in-universe explanation could be that the size of the Jaegers was limited by the ability to control them. Bigger doesn’t always mean better, since one giant robot would require more strength to lift. 
Bigger doesn’t always mean better, since one giant robot would require more strength to lift. 