maybe its my bad english because I dont understand why the problem isnt obvious to anyone.
and yes the problem IS mostly about civics. If you ignore them, there isnt much of a problem. ( least not between farms and towns
)
So lets assume we re NOT running any of these SE boosting civics like Guilds, Scholarship, Agrarianism and Vassalage. Neither did we built the great library.
then a farm (as of patch H ) is suddenly only +1 commerce (from taxation)
and either +2 science (2/3 feeding a sage) or +2 gold (2/3 feeding a merchant),
i.e. the total commerce equivalent would be 3.
meanwhile a cottage/hamlet/village/town is +2/+3/+4/+5 commerce and +1 hammer
Pro´s of cottage economy in this situation:
-once fully matured, a town has almost twice the commerce output of a farm along
with 1 hammer (as of patch H)
Con´s of a cottage economy in this situation:
-a cottage is slightly worse than a farm, a hamlet draws equal in commerce output
but without providing GPP, so until we re talking at least villages there s no advantage until some time has passed.
-no GPP, so while farms have less commerce output in the long run
. they make up with providing GPP and thus later great persons that can be settled , used for golden ages, bulbing a tech or founding a corporation.
I d say in this situation I d definitely go for a balanced mix of specialist and cottage economy.
...
but this situation is one I rarely find myself in.
in the orbis I m playing we have civics like vassalage and agrarianism which greatly improve farms & SE economy and dont have any viable alternative because the others civics in their respective branches are either useless in 95% of situations (city states & isolation ) or at best situationally usefull or not as good as vassalage / agrarianism.
in the orbis I m playing we have the branch that includes guilds, serfdom and caste system which are all 3 viable great choices and guess what ? all 3 (guilds of them the most though) benefit specialist economy somehow.
in the orbis I m playing we have scholarship and the great library
.
here s the stats for the orbis I m playing:
town = 5

1

no civics, no wonders, no nothing ever improves that
(aside from the religious / CoE civic shadow court )
farm = 2

1
vassalage : +1

agrarianism: +1

scholarship: +1/3

per

guilds : +1/3

+ 1/3

per

(feeding a specialist)
end result if running all those civics and feeding a specialist
merchant
+2

+4

+2

i.e. short version: the equivalent of 8!!!!

sage
+2

+1

+5

i.e. short version: the equivalent of 8!!!!

sage with great library built
+2

+1

+7

i.e. short version: the equivalent of 10!!!!
What farms provide over towns:
-instant equivalent of 8

vs 2/3/4/5

, when the farm is built it has FOUR times the

of a cottage and even when that cottage finally becomes a town after many turns, the farm still wins 8 to 5. (or 10:5 with the great library )
-did I mention GPP, you know these points which net you a nifty great person that can be settled, used for a golden age, used to bulb a tech, found a corporation ? you wont get those from running cottages
.
Whats towns provide over farms:
-good money when pillaging them
Summary:
Of course if we assume that the player doesnt use any civics or uses inferior civics then there s a balance between a cottage economy and a specialist one.
Of course you ll not always want to run vassalage, scholarship, agrarianism and guilds together
.. but just one of them is already enough to tip the balance in favour of SE, every further of those civics is merely dancing on the grave of the cottage economy.