It's not quite that simple. If you have food resources, then you have one guy working the resource to allow ~2 specialists. That's 3 against the h/h limit. 2 specialists compared to 3 guys working 3 cottages. (2:3 is better than 1:2).
And, if you're running Representation then you get essentially double the benefit. (changing it to 4:3 or 2:2).
On top of that, before you have a GP farm, if you do it right, then you can generate Great Scientists in parallel, in more than one city. Thus, every city running specialists would generate a Great Scientist, which is worth, oh, 1000-2400 cottage turns (10 cottages for 100-240 turns). Pulling that number out of the air but it's a good benchmark. (As each city generates a GS you could turn off the scientists and change the farms to cottages, if you wanted.)
So, it seems to me, that the higher level you go, the more inclined you should be to specialists and the less to cottages. Certainly in the early game.
Wodan