Isnt the worst of its time basically asking which one is the worst from each era?
NES - FF2 easy
SNES - FF4
PS1 - FF7 (all good, but I like 8 & 9 more)
PS2 - FF12
Havent played enough after that to be able to pick any. Of those above FF2 is still the worst anyways so Id pick that if I had to pick just 1 game period