I like most ideas, though I'm afraid that some do not seem very practical. However I completely agree with the Peace Conference proposal. I always hated the idiotic demands and offers which lead to silly/foolish after war borders or alliance leaders demanding all territory for themselves, thus often screwing the alliance minors. I do think that this will be hard to create though, as a new AI code for that would have to be written.
Maybe they could make it similar as in EUIII, you can see the map and demand provinces on the map, however the negotiations should be done in phases. In every phase the victor demands provinces (or others, like war indemnities, release nation), the defeated can respond by making a counter-proposal, however only if the victor hasn't achieved an unconditional surrender (e.g. total occupation alliance leader, or huge war exhaustion alliance leader).
First after the war has started and the alliance leader feel like its a good time to begin peace negotiation (both victor and defeated) you should for example activate the "peace talks" option in the diplomacy screen. Once both alliance leaders have activated this option, peace negotiations should begin (game pauses). However if one of the alliances has either a very high war exhaustion (>80%) or the war score is very much in favor of one side (>80%) the "defeated" alliance should be forced into peace negotiation.
Once peace negotiations begin the total demands should be based on a score system similar to EUIII. However as every member of the victorious alliance has contributed to the war, based on their individual score (which is determined upon occupied provinces, port blockades, battles fought etc.) they should be allowed to only make demands relative to their contributed share in the war (war score). This means that during the negotiation phase every alliance member sends its proposal to the alliance leader, who will then send the offer to be defeated alliance.
Demands like war indemnities should be distributed according to every member's share in the war score and should be payed by each defeated member also according to the relative to the size of the industry score by the defeated alliance. This would mean that more powerful countries (larger industry, will pay more than smaller industries) pay more.