What I see as the two most disappointing features of civ V are:
1. Incompetent AI, especially at waging war
2. The way global happiness penalties work
2. The severe consequences of conquesting early war as a direct result of the global happiness system
War is honestly a pain in Civ V both from a disappointing standpoint and because of all the penalties for unhappiness and the inevitable unhappiness from really taking out another empire. Most players have gotten used to it but I remember how disappointed everyone was for a few years when the game first came out. You can take a few cities and get hit by over 20-30 unhappiness which is a massive deal early game. Unrealistically the unhappiness hurts science, production, growth, and combat effectiveness of the troops everywhere rather then just locally. It hurts everything and is unavoidable. So you are forced to burn way more cities then previous iterations and stop your own empire from growing effectively. In the end it is manageable sure, especially since you only need capitals, but it's annoying and unrealistic and has a steep learning curve which is a bad design for a game where war was supposed to be a fun feature. With such a great tactical combat system I was very disappointed by 1+2. It really took the fun out of early war for me and it's why so many players are tempted to wait for ideologies to even try. This was a major flaw in my opinion and is a direct result of the way unhappiness works in this game.
I hope civ 6 realized their error and returns to a system where at least some of the penalties for unhappiness are concentrated more locally. Unhappiness and resistance from conquered cities should have regional effects, perhaps even on the garrisoned troops there, but not far away. In fact the opposite was usually true. Rome used war victories and the celebrations after each one to actually keep the population of their empire happy--quite the opposite effect. This is something the honor tree should have really thought about. Perhaps victories could trigger celebrations back in non-puppeted or annexed cities.
I remember long ago that Civilization III had a wonderfully nuanced system for expansion that would be great in combination with 1 UPT. New cities had resistance and corruption, so expanding your empire past a certain point and making colonies far away had little benefit as little of the profit went to the capital without some infrastructure effort to construct police and expand the government (forbidden palace). Also unhappiness from conquest was localized and cities would stage uprisings and return to their previous owner if you didn't leave a large garrison nearby. Also, in contrast to Civ V where burning cities and killing population makes your empire happier, in Civ III if you killed population by burning the city for a few turns or something the unhappiness became more entrenched. Resistance fighters ended quicker but the population had long-lasted unhappiness described as "we cannot forget your cruelty and oppression" if you moused over. Also in civ III you could spend empire funds on entertainment to make the empire happier rather than just being helpless to the global sum of happiness. It felt like a good way to limit large empires but still give many options to players to work on the problems rather then just clicking forward on turns and burning new cities to the ground. However, since there were no global effects to overexpansion ICS was the popular strategy since even though new cities could be close to worthless they didn't ever hurt you unless the had resistance. So I think a combination would be good. Maybe keep the science and culture penalties for empire expansion but adopt the local models of civ III for happiness and subsequent growth, production, science, etc.