People do seem to be focussing their search on a human pilot, but it could be a Pokemon. Either a Porygon as you say, or maybe something like a Rotom.

[This is an Interesting New Thought and is going to require much consideration.]

A pokemon would find it much easier to escape the wreckage and blend into the wild Pokemon. Though, that would still leave us the question of why. I can't imagine a Pokemon would just steal a plane. And where did it get those strange pokemon from?