Manufactories aren't that bad. All GP, even scientists, generally won't repay their settle cost unless you get them very early, that is true. But benefit of manufactories is getting high hammer output without overly harming growth (plant on grasslands). We can praise population growth and science all day, but there is a clear difference between a low-hammer city against a high-hammer city.
The counter-argument is, of course, that if you settle the city in a good location to begin with (horses/cattle, stone, etc) then you can get similar results without needing to work engineer slots and planting GE's.