3)Research. I think at the bare minimum, the layout needs to be tweaked, but I think there could be significant improvement otherwise as well (see next posts).

Layout: How about a wider or taller layout with either columns or rows based on hierarchy? Put all the new ships near each other. Put the defense and regeneration next to one another. Put the added damage items close to one another. I think there was an effort to do this overall, but if things don't relate, I think it is much clearer not to put them in the same row/column.