1) pillaging towns
I think that pillaging towns of newly conquered cities is a wast especially to specialist econ: you have a +4c at min to a +8c +1h at max that is given as a present, pillaging all this hard work is a wast, putting one citizen on the tile will make you lose 0.5 to 1 specialist, but as the town is grown, it is almost worth it, at least in gold production +8c*1.5 (+25%+25% of market+grocer) gives you: 12gpt ==> hop you can transforme 2-3 former merchant + priests into scientist.
2) toward a mixed economy
I think that from the time of printing press: (and latter when Universal suffrage & free speech & emancipation arrives) you should begin slowly the transition from specialist to mixed econ:
-begin to keep the villages and towns of conquered cities
-begin to replace some non efficient tiles/ non worked tiles into cottages in order to start to grow them in non science cities.
-creating some crap cities just to grow the cottages tiles for the big science cities. (not sure if it is anti-gameplay or not, see with your ethic and/or with "anti-exploit hunters", furthermore you can't always afford the rise in city number maintenance.)
-stop working cottages tiles until you have free speech civic.
then it should be nice. (or not)
3) Cabret : study on a full cottage city : farming or cottage-work first?:
I also did some computation following the thread on cottage vs farms, :
my preliminary results are
here in the 1st "Detailed analysis: # of specialist cities needed per era" thread
the conclusion of my little study was that effectively until reaching a certain (unknown, experiment with 2-7-12-max extra food) extra food per turn, it was more interesting to farm and put work on cottages only for extra workers until reaching pop limit.
so even if you have not free speech, you loose less by growing first and cottaging second. with free speech, it might even be as interesting to start as a specialist city running a maximum of cities to max pop, then when free speech convert most of them on cottage workers (on unworked tiles + some on former farm tiles), you are loosing 5 turns per cottage 10 per hamlet: then you have fast growing villages +4c, then 20 turns only until +7 towns
For every town thus obtained you saved 5+10+20=35 turn of cottage-work on the cottage-guy. Furthermore when full grown towns are worst than specialists (equilibrium at printing press) you were working the more efficient specialists. (on the other hand, during 35 turns all your cottages are poorly efficient at a time when you have most improvements so you are loosing much more than the raw commerce... maybe it balances s/o has to try it.

)
4)to another guy: As a specialist economy works with focusing on ... specialists, scientifics even more, even without philo you can easily have obtained the 5 Great scientists requested by the strategy by the renaissance age.