Lower yields "per plant". If youre limited to 4 legal plants for recreation in Canada, then yes, your per harvest yields are going to be shit. But if youre in an area that allows more plants or youve got an ACMPR license(min is 25 plants on a 5gr per day prescription) then that isnt an issue. If you grow enough plants to fill your 4x4 canopy, youre going to get similar yields to growing photos in that same space. Youre yield is limited by canopy size, not per plant yield. I know many experienced growers who choose autos, please dont look at my history here an assume im some sort of noob. Ive been involved in cannabis grows for a lot longer than my post history.
The real disadvantages are potency isnt as high, you need a higher plant count to increase yield, and all plants must be grown from seed, so no clones. Yield is not an issue if you have the plant count, and your annual yield can be increased significantly for far less money on equipment, using half the space. The other downside is once you find a really good pheno, you harvest, you smoke, and its gone forever lol. Maybe not forever, but you could pop 100 seeds and not get that same pheno again.
I knew a dude back in the day growing autos illegally. He went from 4lbs every 75 days with photos, to 4 lbs every 50 days with autos. For someone growing for sale, thats huge.