Autotune is essentially just hovering. If your multirotor cannot hover for more than 2 minutes, that indicates something seriously wrong with your choice of battery, motors/props, etc. Even if your application is something like a racing drone that is pushed to the limit for 2 minutes, it should still get 6-8 minutes on the exact same battery when just hovering in place for autotune.
Can you share your actual setup? Frame design, motors/props/ESCs, battery, total weight, etc. A photo would be great.