Don't reformat the first time until you have at least 1000 investors which is a doubling of app income. When the apps get to 50% idle (maxed out) they will outperform the OS by X3 or X4. Max out the apps, let them run overnight or over the weekend and reformat in the morning. Some apps do slow you down at first, but any maxed out app is always better than not having it; although they do become statistically irrelevant. The first few reformats you can increase investors by an order of magnitude. But then it slows down and you can only double or triple investors each reformat. The stepping stones actually work out quite well.
If I can buy a more expensive upgrade of a specific type I should get all the cheaper ones of the same type without having to click them because the cost is irrelevant. For instance, if I buy 1000 Farms and switch to the upgrade panel I have to click the farm upgrade about 12 times and watch it change colors. Why not click once for Farm 12 which gives me 1-12, then when I buy more buildings I then have to click Farm 13 or whatever the highest tier is I can afford? This should go for all the basic upgrade categories and would reduce the number of upgrade clicks after an abdication from 300ish to 75ish. It is also frustrating to finish clicking all 300 upgrades only to accidentally click Good or Evil when I want to go Neutral, and then have to abdicate and click 300 upgrades again. Some kind of Control-Click option to lock out specific upgrades might be nice too. Especially in light of these new faction challenges.
I think all the Contingency Autocasting needs is a User-Settable timer that allows Autocasting to go 1-2-3-4-4-4-4-4 until time runs out. Then, only the Faceless get screwed with Brainwave. With my meager programming skills I can't think of a way to solve that logic problem. But that's why you're here. :)
Cash per second is only meaningful if all the businesses are paying more than once a second, or at least not too much more than one second. What you folks really want is a cash per longest time unit - usually the oil company. Cash per second of the oil company doesn't tell you anything because the oil company pays you 0 for the first 2 hours and then 20 trillion all at once. Your perceived CPS will actually decline for two hours, and then make and astronomical jump when oil pays, and decline for two hours again. So, no, adding your companies up is not going to tell you how fast your income climbs because they all pay at different rates.
Speaking of pay rate, try to double your business cycles (25, 50, 100, etc) when the time said business is exactly half done. That will maximize your resources and save you hours if y are babysitting the game.
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You may try using the "Multibuy Upgrade Series" option in the Options menu, it should help with your issue.