I can't think of anything I hate about SE IV, just a few annoyances. Most of them have already been mentioned in this thread.
The one that most immediately comes to mind (since I just saw it happen again today):
When ships are abandoned for lack of maintenance, sometimes a satellite group is abandoned, even though sats don't have any maintenance cost.
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Cap'n Q
My first SE IV mod!
Hypermaze quadrant
The most merciful thing in the world, I think, is the inability of the
human mind to correlate all of its contents. We live on a placid
island of ignorance in the midst of black seas of infinity, and it was
not meant that we should go far. -- HP Lovecraft, "The Call of Cthulhu"