It's true that puppets give more gold per turn (due to being locked on gold focus and prioritizing no maintenance cost buildings) than the increased unit costs.
But your unit maintenance cost for 8-9 GS was still more than it was for 8-9 of them for a peaceful 4 city player, and it's the unit maintenance cost (& turn number you win on) that determines optimum last turn for academy and not your net income per turn.
In the strictest sense that is true. However, I am going to argue that unit maintenance is so low relative to the value of a bulb that it is irrelevant and thus maintenance costs should never cause you to decide whether or not you should bulb or plant a GS.
I'm using the unit maintenance costs found at the bottom of this page:
http://civilization.wikia.com/wiki/Mathematics_of_Civilization_V
Let's assume the following hypothetical example:
You have generated 4 great scientists by turn 150, and 8 by turn 200. You save your GSes until turn 200, when you start mass bulbing them for whatever victory condition you are going for (Internet, Globalization, Hubble/science, or Radar for bombers).
In this hypothetical example, you have 30 military units and 10 workers in addition to your GSes.
On turn 150, you have 44 units, so you are paying 89 gpt for unit maintenance. If you planted them all for academies, you would have 40 units, and pay 81 gpt for maintenance. (89-81)/4 = 8/4 = 2. So each GS is costing you 2 gpt at turn 150.
On turn 200, you have 48 units, so you are paying 131 gpt for unit maintenance. If you planted them all for academies, you would have 40 units, and pay 108 gpt for maintenance. (131-108)/8 = 23/8 is basically 3. So each GS is costing you 3 gpt at turn 200.
If we assume that over the turns we are discussing the GSes cost an average of about 2.5 gpt, and you had on average 6 GS, then from turn 150 to turn 200 your GS costs were 50 turns * 6 units * 2.5 gpt/unit = 750 gold. Considering that 1000/1500/2500 faith is considered a reasonable price to pay
per person for great people that you need, 750 gold
total cost for 8 great scientists is
outrageously low. Also, unless you are going Domination, you probably have a smaller army and fewer workers, so your unit costs per GS will be even less.
In addition to gold maintenance costs being irrelevant, I personally feel that the loss of 1 food or production due to planting is also basically irrelevant, as long as you don't block a Civil Service farm. The only things you should consider are: what turn do I expect to win, how many late game bulbs do I need, will I be going Freedom (+4 science obviously makes academies more worthwhile), does the NC city have an observatory, and do I need midgame science to get Renaissance/Industrial wonders or military units more quickly.
I went from planting 3-4 GS per game to planting zero, and I think my games have improved significantly. I might go back to planting one, but I think more than one is probably a mistake.