Galvatron states as a fact that Autobots, as a rule, cannot fly. While this rule has become accepted since then, in earlier episodes, Autobots were shown to be capable of flight. See more
The plague you speak of has visited us once before. A wise man was able to contain the spores, and shoot them into a sun. The only way to fight such madness is with wisdom. Unfortunately, no *one* person now has the wisdom to contain the spores, much less destroy them now that they are spread across the galaxy.
Perhaps there does exist a source of wisdom powerful enough to destroy the spores, and save the galaxy. The accumulated wisdom that resides within the Matrix!