having to set the citys manually one by one when they riot when you change governments. and when you get overpopulation. there should be an auto set that function or do same for all each turn.
But there is.
That said, happiness is assessed before growth during the interturn, so you'll always get 1 free turn to reset citizen happiness before the town riots due to overpopulation. And while your Empire is still relatively small, it shouldn't be too difficult to keep track of which cities are approaching their happiness size-limits.
Admittedly, that does get more difficult as you gain more cities to keep an eye on, but it can still be seen relatively easily e.g. via the F1 screen (rather than having to cycle through all the cities individually) -- especially if you've installed the 'Mood Smileys' Popheads (see the C&C forum and download-libraries). Or (if you've installed it) CivAssistII can be set to tell you both which cities are about to grow, and which will riot on the next interturn, if left to themselves.
For city-management during Anarchy, you also have little excuse. You
know that some/all of your cities are going to riot on the interturn, because that always happens during Revolutions. If you don't want to manually manage each city, you can click into
any city before hitting End-of-Turn (or 'Zoom To' the first city to riot on the interturn), open the Governor, and select Yes in 'All Cities' for 'Manage Citizen Moods' -- which should then prevent (further) riots (if possible).
There are several problems with the city-Governors, though. One is that, rather than simply settling for 'Happy ≥ Unhappy' (which would be enough to prevent riots), they will try and make everyone at least Content -- which often results in food-deficits/ starvation, especially at higher levels where you only get 1 citizen born Content per city. So to minimise shrinkage you'd probably also need to set 'Yes' for 'Emphasise Food', and/or turn off the Governors for any cities that ended up in seriously negative FPT. (Again, you can see this in the F1 screen, and zoom directly to the problem-cities from there).
And the Governors will also turn Unhappy citizens into Clowns, nothing else. So if you want to earn some cash or do some research through the Anarchy, you would still need to reset those Clowns to Geeks or Taxmen yourself. Doing so (IIRC) doesn't force you to switch off the Governor, because you're not altering tile-assignments, but it can still be tedious. The only consolation is that you don't have to zoom to each city to do the Specialist re-assignments, because (with a steady mouse-hand) you can also do these through the F1 screen.