Quickly fixing the political system
Full disclosure: as a person who is a huge fan of political games and following politics in general, I was sorely disappointed by the lack of a true system of politics in Rome II Total War. I frankly think it needs a DLC (preferably a "Free"LC) to overhaul the system with all the features which were almost certainly planned but never implemented for whatever reason. In any case, until that time comes, I believe I've come up with a quick, three-part fix that will at least make the system more interesting, and more crucial to gameplay. Forgive me if it's already been suggested. Here goes my three-part solution.
The quick, patchable, basic, three-part solution
1) Civil Wars should only be triggered if your popularity gets too low, not too high.
By removing the penalties for having too much popularity (which I always felt was counter-intuitive anyway), players will feel free to spend whatever they want to keep their support as high as possible. Low popularity should also be staggered in tiers; for example in an empire system (i.e. not Rome or Carthage) you will have a civil war if you stay at below 50% popularity for 10 turns, 40% for 7 turns, 30% for 5 turns, or 20% for 2 turns (numbers arbitrary and used for example). In republics the numbers would of course be a little different; civil wars triggering perhaps at below 25%, 20%, 15%, and 10%, respectively. Also, and very important: you should receive warnings about an imminent civil war based on your low popularity. "If you stay at this level of unpopularity, your subjects will revolt in X turns." Something like that. Which brings me to the second part...
2) There should be an unlimited number of civil wars.
Ignoring the many well-documented cases of countries having more than one, removing the cap on civil wars keeps the political system relevant late into the game, something that it fails to do now. "But," you might say, "removing the cap creates a new hole in the system. An endless trudge of civil war is an unfun way to keep the system relevant throughout the game." Perhaps, but I think I've found a solution for that, which is...
3)Your house and family members receive a permanent buff to popularity and gravitas, respectively, after every successful civil war.
This last part, I believe, is the real key. Besides the obvious negative incentive of losing the game if you lose the civil war, every successful civil war will give your family a permanent core of court nobles/senators/judges who will always support you. Your faction/family will, in effect, have a popularity floor below which you cannot ever drop. Arbitrarily speaking, every successful civil war should garner an rock-solid, unassailable 3-5% popularity among nobles/judges that can never be taken away (I personally think the specific numbers should be small, but that's just me). These would stack, of course, upon execution of other successful civil wars. Additionally, all future family members should automatically start out with an extra 3-5 gravitas and perhaps some extra authority, some small benefit for being a part of a successful dynasty.
How would the civil war itself work?
Well, it would be pretty simple.
Your side
Your party's generals would join you, of course. Your party's statesmen will be represented by a stack per statesmen at the capital, in the spirit of an influential politician rabble-rousing the people to revolt. The higher the statesmen's gravitas, the better quality and more experienced the stack will be.
A random number of other generals and statesmen would join you (it should probably be a minority of them). Realistically, you would be able to influence which ones joined you but as this is a quick fix, it should just be random.
The opposing side
Most of generals and statesmen who are not in your party will not join you and will therefore be your opponents. Additionally, some extra stacks would spawn at the capital, due to your unpopularity there.
The win condition
Simple: wipe out the other side. Taking the capital should not be an automatic win.
What happens when you win? You receive your buffs, of course. The political system keeps on chugging away with you in a stronger, though by no means invincible, position. Changing from a Republic to an Empire wouldn't present any problems: the politics still apply to you.
Phew! This, altogether, will effectively mean a few things:
1) Without civil wars triggering on high popularity, players will have all the incentives to pump money into their own party without fear of being too popular.
2) The political system will no longer lose all meaning after you win the first civil war.
3) There will be two incentives to win civil wars. First, by building up a core of popularity, you can eventually "civil war-proof" yourself by having an unassailable percentage of support among senators/nobles. This would of course require the successful execution of at least four or five civil wars, no mean feat. Second, winning civil wars means your generals and statesmen will have more gravitas and potentially some more authority, or other personality buffs which makes it worthwhile to win the wars.
This is NOT an absolutely final fix to end all fixes. However, I do think this is a patch-sized fix that will immensely increase the interest in the political system until a potential full overhaul. Speaking of full overhaul...
The dream list for a political system, which probably would require a patch/DLC
This is my pretty ultimate wish list for everything the political system should be. Again, the information above is a barebones fix for the political system which could be implemented in the next patch. But what would a dream political system really look like? Well...
1) It's based on the system I laid out above. Again, that means no civil wars due to high popularity, unlimited civil wars, buffs for party and characters if you win them. I've talked enough about these aspects, no need to ramble on here.
2) You should now have relations with individual characters. Characters, not houses. Each general or statesman not in your house (they're loyal anyways) would have an individual relationship with you. Let's take a look at a general you could interact with. For the purposes of this example, the player is house of Junii.
Lucius Gaius: House of Cornelia
Marriage into your house: +10
Promotion secured by your house: +7
Positive interactions with other members of Cornelia: +6
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Blackmail by your house: -13
Negative interactions with other members of Cornelia -8
Overall: +2
Probability he will join your side in a Civil War: 17%
With individual interactions with generals and statesmen, you can directly influence their chances of declaring for you in Civil Wars. I would just copy and paste the current diplomacy overview, with the excellent pluses and minuses, to the family members. That way you can make plays for powerful generals and statesmen when the time comes. And when does that time come? Well, now that you ask...
2) As a Republic, you should be able to start a Civil War whenever you want. There should literally be a "Civil War Now" button if you are a Republic. Make plays for the right support and cast the die when you're good and ready. Now, I would say that there should be a minimum of 20 years or so between civil wars, but other than that, go for it when you feel like it. By giving players control over when civil wars happen, it would give us incentives to play the political system and amass support.
3) Generals and Statesmen who are indifferent to you shouldn't join the civil war. The guy in my example above will serve us well here. Yes, he is positive at +2, but in my system, he probably wouldn't support you in a civil war. If he were a statesman, he wouldn't rebel, and if he were a general, he would just put his army into "fortify" stance and sit there until the war is over. This would mean that you need to line up your support carefully or risk going it alone.
4) Houses can rebel against you if enough of their characters hate you. If Cornelia hates you enough, their guys can turn against you and rebel. Important to note, one family's feud with another does not count as a civil war. You can't switch to an empire afterwards and there are no buffs awarded. However, winning this feud does mean one important thing: you can eliminate them forever. If the Cornelia rebel against you and you beat them, you have the option to completely eliminate that house for good. This feud would apply to the "other houses" faction, but the option to eliminate them would not. This would also apply to Empires too: if the "other nobles" get too mad at you, they can rebel (but you can't eliminate them). This would be a better late game solution than "civil war at too high popularity." You still have to manage relations with the other factions, instead of just getting power for yourself.
6) Drastically reduced cost of political action. At least in the early game. Lower the cost so we don't have to spend our GDP blackmailing some guy. Lower cost=we do it more=we care more.
5) More. More options for affecting personal relations with characters is a must. "Flatter" and "Offer Marriage Proposal" (why the latter is restricted only to your house is beyond me) are musts. And way, way, way more statesmen for every house in general.
Again, these six points are what I want the political system to be. This would probably require major patches/a DLC, but hey, we can dream. I also think these changes would go a long way to making the system the robust, dynamic, and crucial aspect of the game it very well should be.
tldr: Civil Wars only on low popularity, unlimited civil wars, buffs to faction popularity and character traits when you win them. Later six points are a dream list.
Let me know what you think!
Improving politics
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out of luck. If they control your main army, then you are left with whatever armies your generals are controlling. Senators that rebel should take away from your income. Senators should be given 'control' of regions/settlements. that control does nothing until a civil war, when that settlement will revolt against you, reducing your income, and benefiting the usurpers. Therefore, when a civil war breaks out you can lose access to armies, assets, agents, regions and provinces. This would force you to pay closer attention to the politics and as to who controls what. 
