I have played 340 hours so far and broadly speaking I am enjoying the game, however there are aspects that I am not happy with. All opinion, you may disagree.
1) Crises - utter disaster, I turn them off every game, bit off a pain that they won't stay turned off though.
2) Civilization swapping, and odd leader / civ combinations. All very odd, doesn't make any sense to change from the traditional leader civ combo that stood the test of time. Now we have build something you believe in, but we're going to whip the rug from under your feet twice during the game.
3) Age transition, back to a level playing field. It doesn't matter if you units were level 1, 2, or 3, they will all be level one at the start of the next age. Any lead you bult up will be gone, why bother upgrading units any more than necessary.
4) Graphics overkill, once you cities are developed they take up the map, good luck spotting and railroads once the stations are built.
5) Ally at war, "do you want to be my ally" yes for free, but no is going to cost you, so say yes. Next turn your ally is at war, do you want to support them. No, you don't want to go to war, therefore no longer an ally. Repeat ad infinitum.
6) Religion, just as annoying as before. I don't mind the basics of choosing a religion, and some bonuses that it can provide, but the annoying stream of AI missionaries, constantly converting you cites, leaves the exploration age as little more than a building missionaries age.
7) Feels like there should be 7, so I will finish with, the AI doesn't know when to give up. Current game to leaders keep attacking me, so far this has cost the 7 cities, 2 captured, 5 relinquished in peace deals, in three separate 2 against 1 wars, and still in the exploration age. This highlights the need to see the map, to find out where the city they are offering actually lies, and whether you want it or not, and which other city to ask for instead.