Shields
It may have been covered and i missed it but if the ancients had the technology to create shields for Atlantis surely they would have fit them onto the Puddle Jumpers.
shareHave you just started the show? Due to the size limitations imposed by needing to be small enough to fit through the Stargate, there's physically not room for both a cloak and shield generator. However, by around season 3 Mckay figures out that he can...
modify the cloak to operate as a shield. At first it takes some time to make the switch over, but after he does it once he then does it again much more quickly. Presumably, the Ancients switched back and forth as the situation warranted.