"A plane was flying in the sky."
Oh yeah, を is not a prepositional particle, but に is, so, either Duolingo is incorrect, or the Japanese language has an exception for the way を is sometimes used.
を doesn't literally mean "through," and it would make more sense to me that the particle に would also include the meaning "through," in addition to "in." If I were to literally translate そらをとぶ, I would say that means "fly the sky," which doesn't make any sense in English, but when you use the particle を you are basically saying, "I verb the object; NOT, I verb through/in/at/around the object, so yeah. The way Duolingo used the を confuses the heck out of me.
Some verbs, like 「飛ぶ」are verbs of movement (移動動詞). As a rule, they use 「を」to indicate where they occur, and 「で」to indicate by what means. 「飛行機で空を飛ぶ」("Fly in the sky with an airplane").
This webpage might help you out : http://www.guidetojapanese.org/learn/series/grammar-guide/page/3/
"Across," and "in" are both prepositions, so, I would think に would be the appropriate particle to use.
Maybe just that this sentence has a less chance of popping up? I see another thread asking why を used for 空を飛ぶ.
If anyone having the same question - please just remember one thing: を is not only a particle for direct object, but also for indicating the origin or the waypoint of the moving action.
I question it...big time, because I thought に was the particle to mark prepositions, and I thought を was the particle to mark objects, and it confuses me, if the function of those particles change.
For the structural variations, yes. It is similar to conjugation in European languages. The basic patterns are similar, but they vary depending on the consonant of the ending Kana of the infinitive, i.e. the Bu here.
Politeness is a different concept. But for simplification, we say polite form for the form とびます which is the conjugated part とび followed by the ますsuffix. Politeness actually is not delivered through different conjugation.