Considering how much easier it is to get early farm boosts in ffh(as opposed to vanilla),plus the ability to get unlimited of pretty much any time of specialist you might want, specialist and (perhaps even more so)hybrid economies seem stronger than in vanilla.
While wonders do help(gl, altar, forge/engineer wonder,theater of dreams), none are quite so make or break as the pyramids were. The same is true about civics, where you can run more of a hybrid there as well, rather than having to choose between two civics, one that helps towns and one that gives 3 beakers per specialist. I honestly don't find specialist economies all that much stronger than they were, esp late game(as we are comparing 6 beaker scientists with 6 beaker scientists, and the non scientists are only 2 sci, rather than 3, but prob have extra culture or production), but I feel one of the things that is most strengthened is the ability to run a hybrid economy, even early in the game.
I find due to happiness/upkeep costs, I tend to run hybrids rather than pure specialist economies(except perhaps when trying for altar or culture victories). I like to have a cpl of farms, and a cpl of cottages around even my first towns, so that you get a good bit of the fast growth, but also get the advantage of not needing 1.5 to 2.5 happy/healthy for every tile to get good yields(plus the fact that you can't run unlimited specialists at the start). Only with a few rare civs(bannor or kudorites, perhaps elves), does it seem to make sense to run as a pure cottage economy(and for the elves, even pure cottages turns into a hybrid, though I can see an argument for starting as more of a hybrid even before you get a decent number of ancient forests up, and as they come up transition the farms to cottages).
I'll admit I don't like rexing, which biases me somewhat, but I feel that the way upkeep is setup, the benefits of it with a specialist economy are somewhat outweighed by the costs.
One thing that these arguments have made me aware of is that I prob need to try to beeline Aristocracy a bit more, as it does allow you to run somewhat of a hybrid with just farms(and is easier to transition to from a all farm start if one believes that much stronger than a mixed start). Hate losing the ability to switch to city states though, but the 40% savings does help. It still ends up being less efficient on a per population basis, and early in the game, I find my largest limiting factor is happiness, not how quickly I can grow to max pop. Part of that is I have been aiming for later religions, and avoiding rok, oo and fol with most civs recently, habits I got into from expecting the dwarves/elves to research it for me perhaps.
In summary(since this ran on a bit longer that I expected) I guess I'm saying that I agree that farms are more powerful than cottages(but still less efficient on a per population basis), and that I'm really happy that hybrid economies are not only easier, but seem more natural than the weird situation that vanilla has where it really appears(even if its not 100% true) that you have to pick one or the other.
Edit: One thing I think alot of these arguments are missing, is the fact that specialist(and even hybrids to a lesser extent) lose out in to cottage economies is the efficiency per population(rather than per tile as we are usually looking at it), meaning higher civic costs, higher happiness/health requirements, and probably more cities(and higher costs due to that).