Right now, Stellaris' internal politics model is a bit... dead. There are ethics, which are broad-brush, relatively static popular opinions, but they're too big and slow to change to make it feel like politics is going on - much like the factions, which just sit there giving constant modifiers to your empire. That's cool and all, but politics ought to be about
things happening, on similar timescales to war - weeks and months, not decades. That's where the real action is.
Therefore, I propose a system I'll call 'Political Agendas'. These are ongoing, timed events (on the model of elections) representing political priorities whose 'time has come' - demands for a policy change, calls for pre-emptive war against an alien menace, calls for the
end of said war, sector demands for independence, calls for revolution - that sort of thing. Most likely it would only be possible to have one going at any given time. Pops, factions, and characters would take stances for or against the active Agenda based on their Ethics and (in the case of factions) other priorities. Agendas would have degrees of popular support and opposition - a minor one might only have 10% of the population care about it either way, whereas a massive upheaval will see 90% or more of the population taking a side - which can be modified by spending Influence or by suppressing the pops on one side or the other.
Sometimes it might be possible to choose to resolve an Agenda - generally, carry out/stop the policy proposal within the time limit - at will; at other times, there might be conditions you need to fulfil to either carry out the proposal or prevent it from being automatically carried out, such as getting enough votes in the Senate (ie. bringing the right Factions or characters on-side with influence or bribes) or ensuring your favoured side has more popular support. (Elections would be one obvious example of the latter kind - the Agenda model would handle them very nicely.) The means available to change an Agenda's outcome would vary with your government type and the nature of the Agenda - a military junta might give generals and admirals the ultimate say over the outcome of ordinary Agendas, for example, while a democracy would give votes to Factions proportional to their popular support among citizens with voting rights.
If an Agenda is not going their way, however, Factions with the ability and willingness to do so might choose to escalate matters by initiating protests on planets, reducing production and shifting the balance of the Agenda in their direction. You could then, if you have the right government type, suppress these protests with troops, shifting the balance back - if the generals of the armies are willing to do it. If you order a general to suppress a protest and they refuse, they would thereby shift the Agenda's balance further in the protesting faction's direction.
The decision to start protests would depend upon factors pertinent to the Faction leader's 'loyalty to the system' - that is, the chance would be reduced by their sharing Ethics, particularly on the authoritarian-egalitarian scale, with the government type, by the percentage of their Pops who shared their position (if it's a minor Agenda, only a small percentage of them would actively endorse their Faction's position, with the rest remaining neutral), and especially by their Faction being democratically represented - but increased by their being treated as a second-class citizen, by having a majority of members of their Faction not represented, or by their having opposing Ethics to the government type. A general's decision whether to suppress a protest would depend upon whether they shared or opposed the protesting faction's Ethics and the Ethics of the government type, and whether the empire was at war (they would be more likely to put down unrest during wartime). If the general themselves were a member of the protesting faction, the chances of their not suppressing the protest would be much higher. Naturally, when the government system itself is at stake in the Agenda, many of the factors weighing against protest and refusal to suppress will be nullified.
The conclusion of an Agenda would make the Pops and factions on the side that got its way happier, and on the other side, angrier. Depending on the Agenda, there might be other benefits and risks, too.
Agendas could be initiated by the player spending Influence to launch them, but often they would arise spontaneously - Factions (which under this system would have their own supplies of energy and influence) would spend Influence to kick off their own Agendas. The Influence cost of initiating an Agenda would rise with the population of the empire and hence the number and Influence income of its factions, meaning that the player would never be overwhelmed with Agenda after Agenda hitting their desk. This rising cost would also simulate the difficulty of reforming a massive empire, forcing the player to become more involved in and reliant upon the Faction system as their empire grows. Techs and Traditions would then give the player new ways to manage this growth in difficulty.
Implementing the Agenda system would entail altering the other game systems in two main ways. First of all, changing policies, civics, species rights, and government types - which can be done at will right now, if the player hasn't done it for a while - would need an Agenda. Declaring war might even be subject to Agenda-based approval, under certain war policies. Secondly, rather than happy Factions feeding you a steady stream of Influence, Factions would reward you with lump sums of it from their stockpiles for carrying out Agendas they like - especially ones they initiated. (In order to make this system work, there would have to be a set of repeatable Agendas - policies that last for a set amount of time, possibly replacing some of the current Edicts.)
Moreover, once the game has an espionage system, Agendas - and Factions' attendant functionality - give spies and diplomats something to find out about and interfere in. There are obvious points of potential interaction with @Alblaka's
Diplomacy 3.0 system - the beginning of negotiations might provoke a faction to set an Agenda to oppose the proposal. On top of all that, the ability to set Agendas could open up interesting gameplay choices. A cunning player might rule like Putin, for example - creating and promoting a 'Defeat Alien Menace' agenda, and then going to war with the target, winning popular support and conquering territory.
What this system would do, overall, is to give internal empire politics impact and drama. A change of government would feel like a revolution, rather than the barely-perceptible anticlimax of the current system. The transfer of power in a dictatorship might be as fraught as it is in the real world; contested elections might bring an empire to its knees. Factions would cease to be passive entities to be milked for Influence, and become active entities engaged in changing the direction of your empire. Stellaris' slow midgame would be enlivened by the player's trying to ride the changing winds of politics.
(This system could also be extended further - if a protesting Faction still isn't winning, they might then make the decision to begin a civil war. This would add to the Agenda the removal of the current leadership, and obviously also starts warfare within your borders, with ragtag troops rising up against your forces on planets. The Agenda would not time out until the war is over! Characters and Factions would pick sides in a similar manner to the decision process outlined above for initiating and refusing to suppress protests. The player, too, would have to pick a side to control - their survival in the game would then depend on their side winning. This additional system would be a lot more involved than the Agenda system as a whole, though, and wouldn't be needed to make it work.)