The FET-Stack has lower internal resistance, thus allowing your motor to drain more current, which will discharge your batteries faster. Runtime also depends on the motor, pinion and mechanical resistance.
Providing you go the same speed a 2x3 FET stacks would allow the car to run longer too.
Good old ohms law can be used to explain why the lower resistance will allow more current to travel through the circuit and a higher voltage to the motor.
What it doesn’t explain is power loss. Simply put; a resistor, or device with resistance, is a heater and not a very efficient one at that. So a lower on-state resistance means less power lost due to heat. And even better it’s a two for one deal, since less heat is being generated by the FETs they stay cooler and their resistance stays lower. Unlike a single FET that has a higher resistance which generates more heat which in turn can raise its resistance in a vicious circle.
But these benefits are limited, although the closer to the edge of extinction you push the FETs the more noticeable the benefits become. With a stock motor the increase in speed, torque, and runtime are barely noticeable if at all, especially run time because the FETs shouldn’t be generating much heat (very little power loss). But when you add a motor that pushes the current limit and causes the FETs to get nice and toasty your batteries have to start paying that heating bill.
Providing of course the FETs you used had a lower on-state resistance and where installed correctly with no static damage, heat damage, cold solder joints, etc.
The difference will pretty much be negligible. As was pointed out, the fet stack will be more efficient - which will have fewer power losses - which would indicate that you would get a longer run time. But as was also mentioned, the gain in efficiency will also allow the motor to draw more current, thus shortening the battery life.
Either way, the differences aren't significant enough to care about. There is likely more variation between motors (two x-speed motors are not exactly alike) than the difference we are talking about here.
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