There are some things which are sub-optimal or just plain crappy about Cookie.
Nuclear power plants produce no pollution and as far as I can tell, don't cause problems with land value or crime. Instead of being crammed in a corner hiding behind the industrials, they should be used as padding between the industrials and residentials. The further away those residentials can be from the industrials, the better. Also, the edge of the map is the ideal place for industrials to throw away some pollution for free, so it's wasteful to put the non-polluting nuclear plants there.
The horizontal "stripe" pattern I used for the overall city layout is crappy. The game naturally has a diamond-shaped pattern that every city eventually falls into, where the corners of the city are crappy, and the center "diamond" of the city has better land value. There are places in Cookie where residentials are sitting outside of the diamond and their growth there is horrible. Industrials love it there. The only thing is that introducing diagonal lines to the layout makes things a lot more complicated and you possibly lose some space since it's not quite as easy to optimize as straight lines are. That's actually why I didn't do it from the get-go.
It's also hard to know exactly what the right ratio of R:C:I is, and I still haven't completely figured it out. For example, even in Cookie, if I replace some commercials with industrials, I can usually get a little higher population. This in combination with the diamond issue above is why you see that extra chunk of industrials in the bottom right corner. They were "converted" from languishing residential zones.
I used map 728. Map 61 is a little better. (I think I just picked 728 because I was getting sick of using 61 so much)
Before I always seemed to need to add more power plants as the city got really big, but I finally found a good number that lasted me the entire time: 18.