Well lets say you and Miss Advent wanna team up and pillage my poor planets. I go Hulk rage on yall and kill Miss Advent off in a Leroy Jenkins wave of awesomness.
Now she is a defeted and Ive let loose the horde of Kols upon you. Your like oh snap, lets be friends. Im like Ocean No! I like an elephant I didnt forget your pacts.
Anyhow...long story short, why would AI/players just magically forget teaming up with now dead players?
Lol. I didn't say that the penalty should be immediately dropped, ideally it should slowly decline after you break a treaty until it goes as if you didn't have a treaty in the first place. But you know, if I hold off your hulk rage long enough, Mr. Vasari, who was also at war with Ms. Advent, should eventually get over the fact that I befriended his enemy so we can double team to put you filthy traders in your place. 
If the Devs should happen to listen to me though, don't automatically break all treaties defeated players have. If that player still has a fleet or several planets left when that happens it maybe worthwhile to live with that diplomatic penalty for free access through there remaining defenses.
Are the pirates going to have their random settings fixed? Its really messing up the modding scene for those of us who want caps for our pirates.
Not just for those who want capitals, it's any use of the random settings. The stock pirates go nuts as well.
Okay, so what can we no longer do? 
Btw liking the new avatar there Goafan.
Thank you, I had to use it once I saw it. If I had a holographic computer screen, I would probably look pretty similar to that when playing Sins. 
