I like this idea.  Very well thought out.  Though I'd think that maybe instead of putting a time limit on when the mission can be accepted, the player should be able to accept the mission at any time as long as there's still time in the mission timer.  This way you wouldn't have to babysit the diplomacy window (like the old pirate last-minute bidding).  It'd really suck if you missed accepting a mission you were waiting for because you were fighting off an opponent on a much needed planet.

And I'm guessing no response at all to the mission counts as a refusal of the mission?

Yep, pretty good idea!

works for me, but I'm not so sure abut the automatic cease fire idea. It just doesnt make sense to me that a long standing rival empire would just stop shooting so a little task can be done but aside from that yeah thats alright, but maybe no time limit on acceptng because quite often in sins you might be too busy to look at the diplomacy panel everytime one pops up

i like all those ideas, but i would like to be able to trade technologies with my allies and more espionage other than just sending ships to a certain location

Need more rewards: Trading ships (i.e. TEC player gives Advent player a Marza, 10 Hoshikos, and a carrier, at the expense of the Advent fleet points or TEC fleet points, depending...); Trading tech (Armor/HP/Shield...) (These can't be taken back... one can select what techs to give); Share structures (like Phase Gates and repair); Share fleet points (one player runs econ, the other military. The econ guy gifts the fleet points to the military guy who does with it what he wants. Can include both race's ships in the fleet, it's just all under one person's control. Although I'd be the only one to do this...)

culture bonuses affect multiple empires (so 3 Advent players allied = 18% mitigation, 3 Vasari = 45% damage... maybe not just a straight stack, but you get the idea. This only takes place where all three culture areas overlap.); Culture can meld in with other culture, not just shove it around.

Not sure about the cease fire... perhaps if the time to complete mission was shortened drastically (halved?), and the time to offer mission was kept the same as it is now.

How about "Help Me" missions? especially easy to complete as Vasari with phase gates all over the place (Kotsura!)

Yes you got it.  The whole point is the cease fire.  The idea of asking another empire to help you out by giving you some credits or undertaking a hazardous mission to attack one of your enemies, while attacking the empire you are requesting aid from doesn't seem right.  Attacking his ships as he in on his way to put a hurtin on your enemy at your request does not seem like a good idea either.  There are plenty of enemies in Sins, so the missions are an attempt to find out who you will beable to work with and who you can't.  As the race shows a desire to work with yours and completes meaningful missions for you, diplomacy improves and eventually leads to alliance against a common foe, even if temporarily. 

The cease fire also makes this a big deal and strategic in nature.   You might accept the mission just to get the cease fire, or refuse it for the same reason.  It makes diplomacy immedately strategic in nature.

I was looking for something that may be easy for the develpers to implement yet provide a big benefit to the game.