You can still conquer large empires. You just have to consolidate and develop your conquests or they will split apart. Just like Genghis Khan's empire did. Remember that allowing small civil wars to happen helps prevent large ones.
I tried this out on a Noble, Huge Earth Scenario Map as Genghis Khan of the Mongols in their historical location. Genghis initially built a Classical empire of 20 cities. At this point, without any Dissent-reducing buildings, the Dissent from pretty much any choice of civics was negligible. Genghis then entered a Medieval Great Golden Age, and expanded by conquest and settlement to 43 cities.
It is very satisfying to use a Golden Age for a rapid expansion, although it seems weird that Dissent goes from 0 to enormous at the end of a Golden Age. Everybody was completely content for a very long time and then everybody instantly became discontented. The no-Dissent-during-a-Golden-Age benefit has the side-effect that it is not really possible to see what Dissent will be until the Golden Age is over. Perhaps this benefit should be removed.
At the end of the Golden Age, the empire is stuck. We still have no Dissent-reducing buildings available. Dissent means that the only viable civics are the most basic, Iron Age ones. Using more advanced civics makes Dissent rise so fast in all cities that empire-wide Civil War quickly ensues, and even if all the rebels can be clobbered and the Dissent clock is reset, it will all happen again soon. Genghis' problem is not a little provincial Civil War, but an empire-wide one that will quickly recur.
But there is nothing wrong with the empire except that it is very successful. It is powerful and could easily eat its rivals. All its cities are very very happy (net 10-26 Happy faces) and very very Healthy (net 9-25 Healthy faces), but these factors contribute little to suppressing Dissent, especially when compared to the negative effects of a second religion. What's not to like about being Mongol? We even pumped up our rivals' Dissent by exporting religion to them so that un-Happy-ness contributes to Civil War splitting them up. And they are half our size! We can make them even more miserable by exporting other religions to them and there is nothing that they can do about it. We know for certain that they are miserable because we can look right into their cities.
Apart from conquest, Genghis looks left and right and sees many great locations for settling new cities right next to the empire's existing boundaries. There is plenty of unsettled land. But nope, expansion is impossible. We just have to let that land lie fallow, for centuries. Geography means that most of it won't become occupied by other civilizations. (So when in history has accessible fertile land
not been colonised by somebody?)
Without resorting to genocide, the game is now a long clickthrough until some technologies unlock buildings to reduce Dissent. But, even after we build these buildings, at each stage, the problem begins again, just notched up in scale a little. There is, at each technological level, a cap on empire size.
This isn't fun because there is no strategy involved. Happy and Health caps work well because there are usually other play-choices than letting a city grow, and because the player can make strategic choices to address the caps. For instance, why can't Genghis address Dissent with larger garrisons? He's more than willing to pay the soldiers their worth! He would be willing to pay City Watch or Spy or Police or Secret Police units if they suppressed Dissent.
I have attached a Save of the situation at 704CE, with 43 cities, 2 turns before the end of a Golden Age. I would appreciate it if anyone could play it through and suggest alternatives to me on how to continue.
I can't actually add new custom game options like that. 'Fewer Religions' was an exception because it replaced 'Choose Religion', which had become obsolete.
Doesn't the list containing "Choose Religion" contain other options that could be replaced? A particularly ahistorical example is "One-City Challenge". Anybody who wants to play with just one city can surely just use self-control to do so.
You're welcome to modify CivilWar.py to adjust or disable it yourself though. All the relevant values are labelled near the top of the file.
I have previously nerfed Dissent doing precisely this. Doing so currently seems to generate a slew of Python warnings at the beginning of each turn. (OK, maybe that's my ignorance of Python.) The warnings make the screen hard to see but I don't know whether they mean anything serious.
This solution is also unsatisfactory in that it needs to be reimplemented with each new version, and I can't easily remember the settings at each point. Is it possible to embed a Dissent-strength slider as a parameter in that CivilWar.py code? Say, define a real number multiplier between 0 and 1 for the strength of Dissent from none to full in CivilWar.py?