We all know how frustrating it can be when you think you've got a good thing going only for an unexpected flip or spawn to ruin a large part of your empire. Certainly this gets better as you get more experienced in the mod and learn how its mechanics work and when, where and under what circumstances flips and spawns happen, but when you're new to the mod or playing a civ whose history you know little about, such events coming out of nowhere can be discouraging. I have seen first hand how a friend of mine got turned off from playing this mod after he lost half of his Roman empire to the Byzantine spawn and then lose almost all of his troops to desertion when he tried to reconquer the east.
I therefore suggest that, at least when you are playing on the easiest difficulty (as you probably will when you are brand new), the human player gets warning popups before a major event that is going to negatively impact them is about to happen, say ten turns in advance. Obvious examples would be the Mongol spawn when you are China or Korea, European conquerors when you are Native American or Alexander's conquests when you are Egypt, Babylon or Persia.
Of course we can do better than just having the game tell you with no bells and whistles "yo stuff is about to happen that you should prepare for". If we look at Fall From Heaven II for inspiration, when the Armageddon counter passes certain points you get nice flavorful popups telling you for instance that if you foolish mortals don't stop sinning soon you are going to invite far darker beings onto this plane of existence than you can handle, with the first such popup being an advance warning and only subsequent ones coming along with actual negative effects. With some creativity we can turn contrived, frustrating and unexpected game mechanics surprising you out of nowhere into ominously foreshadowed flavorful adventures! These messages could even give you a subtle hint of what would likely be the best course of action, i.e. strengthening defenses against conqueror events or abandoning doomed regions that will soon flip.
Imagine you are playing Persia and it's 400 BC. Suddenly you receive this message: "Travelers from the west report that one of the accursed Greek tribes, the so called Macedonians, have in a shockingly short amount of time made massive improvements to their military infrastructure and training and are currently in the process of taking over all of Greece. Many worry that their rapid expansion will not stop there and that they will seek to conquer our mighty empire once they are ready. Your generals urge you to build up your own military and strengthen the western garrisons. They especially caution you about the dangers of the famed heavy infantry the Greeks are known to field."
For China it could be something about the commanders of your northern garrisons warning you about the increasing level of organization the Mongols seem to develop, advising you to strengthen your defenses, especially against cavalry, in your most important cities in easily defendable positions, but to abandon outlying desert towns as they are likely not worth the cost of trying to hold them, especially since the local population is getting increasingly rebellious as it is.
For the Native Americans it could be something like "Your oracles are prophesizing that the end is nigh and the gods themselves will arrive within our lifetime to strike us down if we are not prepared", with the warning popping up when the first non-American civ has researched Caravels.
And now, for a completely unrelated suggestion, how about enabling espionage against Independents along with certain special actions like negotiating trade and open borders or decreasing the likelihood of any given unit deserting to a newly spawned civ depending on how much espionage you have against Independents?