I've been thinking about this, and there's a few things that I don't see on the list that I think should be there.
1) penalty for you having a military force/starbase in/very close to their territory. Maybe only computed at construction time for starbases. While I'm sure the AI will take that into consideration in deciding its actions, I think it should color relations as well.
2) same for cultural starbases.
3) Penalty for my voting against you on a United Planets issue (so if I say that the Arceans should have to pay 7% of their income to everyone else, the Arceans should not be happy with me, or at least a little less happy).
4) bonus for my voting in favor of you on a UP issue.
(and no, I don't know how to count multi-answer issues, like "who gets the expo."
As for war not fading, sorry, even that fades, just not as slowly. Do the US and Britain look like they're still upset over that little civil war? More recently, I don't think there's a lot of animosity in the US towards Japan, Germany, or Italy over WWII.
I'm pretty sure that Yor penalty is if one person is the Yor and the other isn't. In other words, the Yor will have lower relations with all other races, and it will be reciprocal.
On a tangentally related note: The AI needs to take a few more things into consideration when deciding when to declare war. Sure, it's easy to say "my military is bigger, my economy isn't too much weaker, I can win." but if you're overlooking the fact that the person you're declaring war on is the technology leader, or even a technology equal with a lot of cash in the bank, you have to be prepared for that person to either have enough cash laying around to BUY a fleet in a single turn that makes you feel quite a bit less secure, or be willing to shake a few techs loose for cash to all the other players, and THEN buy the huge fleet. I often go from having a military a third the size of the attacker when war is declared to a 50-100% advantage the very next turn.