I didn't notice a thread about these issues in the first pages and I didn't want to necro an older one, so here goes a fresh list:

1. Military Actions.
These should not be permanent. When I manage to make an AI angry with me for fighting over neutral planets a couple of times or smacking his ally once or twice, after which I get -10 military actions penalty towards him, there is no way on earth to recover from that, ever. No way, maybe except making 40 envoys and flooding the enemy's planets from all directions, hoping that he doesn't wipe them all before you rack +9 envoy bonus and manage to get a ceasefire. This is still a lost cause however, because envoy bonuses decay quickly and are capped per planet, while military actions penalty does not decay nor is it capped (not on any reasonable level at least). You might also try killing the AI's enemies but unless you want to try killing yourself (the AI's worst enemy ^^), this usually means having to fly across the AI's territory to his other border, which is a bad idea in general.

All in all, once the AI goes into a blood frenzy, there's no stopping it.

I think "military actions" bonuses should decay over time. Maybe not completely, down to +/-1.0 or +/-2.0 (or maybe 3, 4? some reasonable level that you can somehow manage to overcome). It is perfectly sensible - over time the memory of your help/aggression may not be completely lost, but should be somewhat forgotten/forgiven. It is ridiculous though that once you rack up 8 or 10 negative points of military actions there is just no way to recover from that and the AI will be your blood enemy until the Universe collapses.

It is an worthwhile argument that maybe sometimes a player simply WANTS to kill, not hug you. In this case I suggest that "diplomatical inclination" bonus starts as it does now (between -2 and 2) but is then made somewhat 'mobile'. For example, an AI who started with a positive inclination of 2 points might decide later in the game that you're the most juicy target around - in which case the inclination would drop to -5.0 points for no other reason than simply because the AI wants to go to war with you (which is pretty valid a reason in this game ).

Either way, Military actions bonus should not be permanent. Three hours of doing NO offensive move towards an AI should reduce its hatred towards you, which was caused by some skirmish three-and-a-half hours ago, to an extent at least.

2. Rightclick Planet ICON = fly there (not necessarily 'use your abilities on it').
When you select an Envoy which has an ability researched that requires it to get point-blank with a planet to activate (like the Vasari's planet immunity or planet heal), I think that clicking on a planet ICON should NOT be translated as an order to use its planet-targetted ability.

Although you might think it makes sense, it does more evil than good. Most of the time when you click on a planet icon, you either want the envoy to just go there or you want to mark the planet as a waypoint to another. Either way, if the envoy decides that it has to use its planet-targetted ability it is generally a waste of time or an outright threat to the envoy's existence.
Sure, when I click on the planet itself (zoom in to see the gravwell and click planet) then there's no doubt as to what I want the envoy to do. When I leave the envoy in a gravwell with the ability on autocast, then there is no doubt either.
But just as clicking on a planet icon while having a cap selected does NOT issue a "bombard planet" order (just a "fly there" order instead), the envoy should not understand it as a "use ability" order as well.

3. Goodwill tooltip.
The Goodwill ability tooltip (or Vasari envoy at least) is misleading. It sounds as if it affected all neighboring planets, as in all planets connected to this one with a phase lane. Of course, it does not.

As a side note, it might be a decent idea to make it work as the tooltip implies. For example, you might add a tier-6/7 tech "Convincing Messages" that allows envoys' goodwill ability to affect neighboring planets as well (with a severely nerfed efficiency, like up to 0.2 diplomatical bonus max and a reduced ratio). This might be another way of establishing diplomatical relations with AIs who RELLAY OMFG HAET U (look first point) and to whom you cannot send emissaries directly (cause they would be grinded on sight).

4. Distant Players - Distant Business.
While it is way too hard to make a ceasefire with your neighbours (point one again), it is way too easy to make alliances all over the galaxy. Other factions send you missions that you do automatically (like, kill ships of <insert the guy you're fighting anyway> ) and you receive military action BONUS for fighting your blood-frenzied neighbours (who are likely enemies of their own neighbours, so according to "my enemy's enemy is my...").
However, as much as it may sound sensible again, it is almost a cheat in Diplomacy. That's because once you've worked out a ceasefire with that guy on the other side of the galaxy, you can send/escort a pack of envoys there to secure a 15-point relationship and this player is not going to be your enemy EVER AGAIN unless YOU want him to.

So basically once you deal with your immediate neighbours who will likely stack -10 military action penalty before you can counter it, the whole galaxy is going to be your loving friends with almost ZERO effort. You can then proceed to pacify the remaining AI players one by one while making sure (by establishing overwhelming envoy presence) that others don't object too much. OR, if you're playing with diplomatic victory ON, you just wait and automatically win.

I believe that something has to be done to ensure that distant AI's cannot be turned into loving friends too easily. I am yet to figure a simple idea to fix that though.