I want more things to negotiate over. It feels too much like a marketplace than anything diplomatic. We need to discuss other factions, where the pirates are, or the Dread Lords. We should talk about who is in the lead in snarky tones. We should plot against other factions with trade embargoes, deliberate price gouging, espionage sharing, etc.
Definitely, active military cooperation and planning with one another needs to be available. Falling into a snare of individual treaties with collective Galactic War implications should always be an easy danger. The game has a military emphasis built in. It needs military discussions to be an emphasis as well if the Diplomacy is going to seem relevant to what is going on. You also need a foundation for the "gang up on the leader" principle. For Malevolent factions, "gang up on the weak" needs to be available as well. Though it will have serious Diplomatic repercussions. A lot of the Diplomacy will favor Benevolent behavior, but that is the traditional nature of institutions like the UP, unless the Malevolent folk ramrod their way into power. 
I want Ideology to get much more involved. I have a thought of an events system called Diplomatic Opportunities. You would get chances to do something based on relative Ideologies: agreeing to denounce opposing Ideologies, or increase the value of your own, permanent trade benefits, whatever. Ideology should affect Diplomatic deals and be obviously documented as to how it is affecting those deals. There should be opportunities to align more closely in Ideology. One Diplomatic Opportunity would be a chance to do something like re-lock one Ideology perk that the other faction doesn't like and adopt one available perk of equal or lesser value in their Ideology. You get whatever you bargained for it in the deal, and then you get a one time large Diplomacy bonus with that faction. There could be some Diplomacy deals that have Ideology point results, Benevolent for aiding weak factions, Pragmatic for making loans to weak factions, Malevolent for demanding tribute, etc.
There should be a concept of Prevailing Ideology that is a measure of how many Ideology points you have put into any one choice versus the other two. The tendency should be for Prevailing Ideology values to converge as a basis for alliances and trade groups. This should help build game-long narratives. You could even establish a Galactic Prevailing Ideology for the UP to adopt.
Whatever I do diplomatically, it should be documented in my Diplomacy window with that faction. I should never be ignorant of anything I am negotiating or discussing. That includes my own economy.
I hate bringing up mechanics from other games, but one of the few things I really enjoyed about Civ 5 was their Diplomatic proposal and vote system, with two competing proposals going on at once. I got a lot of variation of results and decisions out of that. It argues for the concept of knowing what the proposal is going to be for several turns before voting on it, and then implementing negotiating for votes.
The UP needs some teeth. Not participating in the UP should be bad. Defying the UP should be devastating. Kicking someone out of the UP should be possible, but very difficult. Peacekeeper actions should be a possibility if some faction is beating up another, especially if you are building up a resistance alliance against a runaway faction. Planetary influence radii should be affected by faction UP standings. If you collapse a faction's influence circles for being a Pariah, they will lose a lot of asteroid mines.
I think that membership in the UP should be a one time decision with severe penalties for backing out. Membership should have benefits. I like 5% per era for Approval and Production, sort of a reverse Coercion. Trade deals between members would have diplomacy discounts. Trade deals between non members would be normal. Trade deals between members and non members would come with price hikes for the non members. That could become a source for political grouping as well.
But there should be an option for those who don't want the rules and restrictions of the UP, just not a pretty one.
Most of all, I need a Diplomacy screen that efficiently deals with 100 factions. I don't do all that many factions these days. But when I have tried >20, I can no longer keep them straight. I should have icons, leader names, faction names, whatever, easily visible so I can keep them straight. I should at least be able to sort them in alphabetical order, for goodness sake. And that should be true for the faction selection list at the start of the game, while I am ranting on the subject. I have >150 subscribed factions from the Workshop. You don't even sort out the stock factions to select, let alone put my favorite custom faction in a convenient place. I truly do not understand that particular inconvenient oversight. It is even worse trying to deal with the faction list in MP settings. So please, look at things as supporting those 100 factions in a Diplomacy screen and I might have the tools to start keeping track of 20. Otherwise, I just can't deal with it and cannot play the game to the levels you suggest according to map size.
Sorry if this got a little long, but you did ask. 
