I guess I don't pay attention too much to dialogue boxes on my kindles. I find them to look a bit cleaner now with the new update. I can't say I ever looked in the setting for my device name once I named it. All my kindles have names.
I have a nice X on my search box. I can't find anything wrong with my X

Is it larger now? Its there, I can hit it with my touch screen challenged fingers, I am happy.
It things bug you, send an email to the feedback email at amazon. My Oasis and Voyage are running very snappy now. But to be fair, they always tend to be a tad snappier after a update. Probably cleans out some slow juice.
I really like the darker text in home view. I like the new setting look. But I didn't really have any issues with how that was before.
I don't read Manga, not really sure what that is, I assume they are comic books? So I won't notice anything on that front as I don't read comic books.