Hey, uploading a save from the future eras, where slowdowns are harsh, with 1-3 minute turn times. Within the last few turns, i thought the game froze because turns were so long.
Note on the save, i mod my civ just a tad, so some traits are different. Also, this should be the latest SVN as of a few hours ago.
Side note, how do i build sea tunnels?
That's actually what I'd expect for late game on a large map. Anyway, I ran your save through the turn profiler, and the major cost is cities deciding on what to build next - it's taking approximately 0.1 seconds per city, and with about 450 cities in your game it adds up. This is not totally unaddressable, but there isn't any really low-hanging fruit here.
Edit - incidentally this cost is proportional to the total number of cities (obviously) and the number of buildings that can be built at your current tech level. The latter factor is why it gets worse in the late game especially, and also why it gets worse in C2C generally over releases as more buildings are added. I'll add a TODO item in the issue tracker to work on this a bit (I think I can crack it substantially given a couple of days to spend on it)