Good points and illustration. I think that there is no true need to be able to empathize with alien intelligence in a narrative. Goodness knows I have trouble empathizing with plenty of human characters... Hierarchy of Foreignness was even a thematic element in the Ender books.
Have you read A Fire Upon the Deep by Vernor Vinge? I remember it doing a pretty good job of imagining polymorphic sentience and civilization churn.
Heroics. The fate of the society/world/universe turns on the actions of one or a few characters.
Heroics only make sense in certain settings. In many/most, it really doesn't make sense for the main characters to be the primary plot drivers when there are millions or billions of other actors in the world. I think it is overused, presents a tunnel-vision worldview, and ultimately confines the world to the characters and ends up less interesting for it.