there are no enemies that require you to have a specific baby to defeat them in this game so idk what you mean
like, everyone say, red fly, if you not have a throw baby, only shoot it, one or two wave will be fine, but when you need face more enemies, it up→flyyyyyyyyyyyyyyyyyyyyyyyy→down, and you will lost, so you must have a throw baby
for PVZ2, the fly zombies, they up→fly→down, one by one, whether it face a whole line plants or interval plants, so even if you only have shoot plant, you still can defeat fly zombie
"'ve just never encountered this problem" is not mean this problem is not existent, and i am not sure what you mean " block the enemies that block your shots", you mean kill that? Or use some baby like "Cube of Meat"? Whatever which is you choose, they all lead to you place more baby in a line and plums will easy to fly