I will give you advice that Firaxis has ignored for a couple years and believe me, I know a thing or two about workers.
One of the most problematic deficiencies on huge maps is the workers AI. (And, I use the word AI real loose here cause there really is no AI in this game and this is not a slam on the product, it's really about the definition of intelligence that one applies, it's most likely my opinion and mine alone so chill.)
Every worker that is automated, both your workers and the AI's workers, does an extensive search for squares to improve in it's territory and ways to join disjointed territories together on the same land mass. So, if there are alot of automated workers in the game, turns take an extremely long time (they will search each and every tile on the map that adjoins it, for a job and there can be alot of tiles to search, thousand on a huge map). Part of the problem extends to the fact that if a worker cannot find a job to do it will then go to a city and wait till next turn to try and find a job to do next turn. Even if a worker cannot find a job to do, the search for a job is repeated by each and every worker by that player even if no job was found be the previous worker of that player, that's known as redundant search!!, so if you have hundreds of workers and the HOFer's know what I mean, it's coffee break time. Hence, long searches for jobs by workers ,on really big maps, that they can do (programmers, feel free to apply liberal if then else's; right here) are a real weak spot in the time consumption of the processor in this game. (Yes animations are high up there but in these instances, they far outweigh even animation concerns)
I, personally only automate workers, generally, once railroad links across my territory are established (as a time saving measure over manual manipulation of massive numbers of workers), once workers start converging in cities without any work to do, I then join them into existing cities or repair work that the automated workers have made based on my objectives at that time.
You can save alot of time on turns on huge maps by reducing the number of automated workers looking for jobs, or waiting in cites for jobs by joining them to cities. Even if you keep a few automated workers around to reduce pollution, toward then end of the game, you will find that the difference in turn play having 10 rather than 20 automated workers an amazing increase in speed (easy verifiable hint to testers).
So, the moral of the story here is to reduce your automated workers and that of your opponents (by conquest, if required , and the most direct course of action that is available to you, by the way) when you really want to speed up the game.
Might not help you but maybe someone else.
