There is a measure by me called "increase in IPH per upgrade time", in other words "income acceleration" IA.
By upgrading buildings that have the highest of this measure, your IPH will increase the fastest - PROVIDED there is no waiting for saving up enough.

There is also another measure, the "popular one" and seems to be the only widely known one. It's called "return on investment" or ROI, this is about "income increase per cost", but I won't go into this because it's simply one of the straight up WRONG way to go, and were here to WIN! >:]

If time is your limiting factor*, not money - go after IA. (*i.e. money is not a problem)
If vice versa - go after ROI. (This applies in the very early stages of the game, when you have to save up for anything you want to buy, that's why it doesn't apply to our case.)

I personally go with upgrading the one giving the highest IA - that I can afford!


The formula for IA is: [income increase]/[upg time]
And is derived by dividing (1) by the upg. time getting (2):
(1) (On-Oo)/Tc = (In-Io) = [income increase]
(2) ((On-Oo)/Tc)/Tu = (In-Io)/Tu = [income increase]/[upg time]

Oo = output old (cash)
On = output new (cash)
Io = income old (income per hour)
In = income new (income per hour)
Tc = cycle time (collect cycle in hours)
Tu = upgrade time (hours)

I personally think the below 1h ones are way too tedious!
The faster cycle time a building has, the more you'll lose by not collecting perfectly on time, so they're less efficient. A building that's not collected is equal to idling, it's not producing any money. Because of this they are compensated with a much higher IPH than the longer time buildings, but this is theoretical IPH provided you collect perfectly on time! So your IPH stat becomes very inflated by these buildings, not reflecting you effective/actual IPH.



I have a model for calculating a more* realistic IPH by looking at what happens during a whole day:
(*I'm not going all out on every little detail here, just the few biggest factors)


1hB: Starting with 1 hour buildings. (Until very recently I skipped these too.)
Originating from myself, I'm assuming these will be collected 6 times per day. That is 6 visits to the game that all are more than 60m apart. That equals 6 collections, which equals the building producing 6h out of 24h. So over a day that's 6/24 = 1/4 of it's IPH.
Hence I detract 3/4 or 75% of the 1hB IPH.

0.5hB or 30mB: Also 6 collections, producing 3/24 hours so effective IPH is 1/8.

5mB: With 6 collections, producing 0.5/24 hours, 1/48.


3hB: Next is 3h buildings.
Now, and going forward, assume also sleep of 8-9h.
Worst case scenario is you sleep right before collection, this means 9h of idling.
Best case scenario is you collect right before going to sleep, which means 6h of idling (since the building produces the first 3h into your sleep).
But anything in between can also happen, so I take the average: (6+9)/2=7.5 which divided by 24h is 0.3125
Since you noticed I like to underestimate, say this is 1/3 or 0.33 that I detract from IPH.

6hB:
Worst case: 9h idling.
Best case: 3h idling.
Avg is 6h which is 1/4 of a whole day.

8+hB: Eight hour buildings I don't feel like punishing, same goes for longer cycle buildings.





So now that I've gone through the foundation, here's some more concrete instructions:

0. You will need lots of expansion area, clear it up by selling decorations (completely pointless) and those 1h or less buildings! (Unless you put in several days of upgrade time into it.)
Wait with expanding if you're not in immediate lack of space to save money.
As for layout, I have the buildings sorted after size, in rows, easiest way to not leave gaps, feel free to visit me =) -will post a pic.

1. There's absolutely no excuse to not have two of each money building!
(The vast majority of bases I see in the game, 90%+, have around half of all buildings!!)
Make sure to get 2 of each and every money building FIRST!
This is because IA is the highest when getting a building, and drops off fast as you upgrade (are a couple exceptions).
The 1h or less have lowest priority and are excluded from this rule.
Infact, their priority is below def buildings because of the area.
Also, the 3h buildings have somewhat lower priority.


2. Start upgrading buildings by choosing the one with highest IA that you can afford.
You want to avoid having "gaps" in IA (i.e. IA being zero), e.g. plan your timings somewhat to not have an upgrade finish in the middle of sleep.
Some IA is better than none. And waiting a longer time to upgrade a high IA building is basically in all cases worse than by instead using that idle time upgrading a building with slightly lower IA.



Here's my personal spreadsheet...hope this works...
This one includes an adjustment: 1h buildings suffer a 75% output penalty, 3h 33% and 6h a 25% penalty. This is my way of "leveling the playing field". Going by this, you can ignore the 1h and 3h buildings having lower priority...




Tell me what you think!
Ask any questions!
And good luck fellas!