JR expressly state that using a 3S lipo will invalidate their warranty, Futaba don't but it's still not such a good idea, especially when running 2.4GHz.
Most radios will tolerate a 3S lipo okay but some will inevitably fail due to overheated regulators.
Putting a couple of diodes in series with a 3S lipo will drop the voltage by about 1.2-1.4V to a maximum of about 11V when fully charged and around 10V for much of the charge -- which is within most manufacturers' specifications.
However, lipos are not without their other issues -- such as the ever-present fire danger and the worry that if you leave your radio on unintentionally and the battery goes flat -- it's probably going to be stuffed.
That's why I opted for the protected cells -- they're not likely to go bang through overcharging (they just disconnect themselves) and you can't over-discharge them because again, they disconnect themselves when they reach the minimum safe operating voltage.