I don't get why they don't have both fans run the same speed as dictated by the exhaust temperature. To have the intake fan run slower because it's cooler means, I'm guessing here, less efficient air flow. If the slower fan is getting help from the draw of the faster fan it's just a bigger load on the faster fan.
If you aren't too concerned about noise or a little extra power, you could do the "blue wire mod" - i.e. clip it - and it'll run full speed all the time.