You forget that Sins ain't a pure 4X and it ain't a pure RTS either.

What you ask is simply too difficult (if not impossible) to implement in an RTS as Sins, can you imagine having 8 A.I.s (as you mentioned) all wanting a different planet from you?
Those diplomacy options that you describe are simply too time consuming for an RTS.

The missions system is the only way they could bring some aspects of 4X diplomacy within the limited time confines of an RTS. Initially they will be missions like "give me some crystal" while later there will be more complex and difficult missions with a greater reward.

Don't forget that the other factions can't really threaten you, they are already your enemies (so what they will kill you differently?) so it is up to you to decide which one you will become friends with while you destroy the other factions.

The only problem i have with this diplomacy model is that you can't win an Allied victory in an unlocked teams game.

The diplomacy is quite unlike any other game I've played, but it does work. If you look at it like a game of the ancient classic "Master of Magic" there are some similarities. The main difference is that you don't get a free choice of which AI you will court with gifts of resources. The AI will make their requests/demands and if you want an alliance you can get one if you fill the early resource demands promptly.

If you aren't fast enough to start handing over resources you miss the boat and the attack missions come out. Those could perhaps use some more tuning, but they are not disastrous, especially for a faction with access to diplomacy bonuses in their research tree. If you miss the easy resource missions though you won't be able to raise the AI disposition far enough fast enough to get a trade pact from your neighbours. If you score the trade pact and have enough trade stations in place you usually get a ceasefire if not a full alliance, because the AI will value the trade income.

The wartime part of an alliance works reasonably well, with the AI ally providing good information on their own defensive needs. I haven't really tried to get the hang of using pings to direct the AI to make attacks on my behalf, but they often turn up to help in battles anyway and that's good.

The part that works less well is the AI choice of targets. I'm not likely to divert my forces in a tight fight to destroying an arbitrary number of civilian facilities... but often the timelimit for the mission expires during the closing stages of the battle for the system - so I'd have had to switch to hitting the AI's goals far too early and probably I'd lose the battle if I cooperated.

One possibility would be to introduce partial credit - so if the AI wants me to destroy six things and I get one, I get less credit. I think it could be weighted so that the first and the last targets give a bigger share of the spread from -X to +2X reputation and that might make the AI response quite interesting.

Also, what about making the AI goals a little more specific? If the AI is under culture threat perhaps it could ask for not just "6 civil structures" but "these 3 culture-spreaders". Combined with the partial-credit system that might go a long way to letting the AI use the player to achieve the AI's real strategic goals instead of doing fairly random make-work.

Still, the system is quite playable even now. It does seem a bit raw, but there's untapped potential too I think.