When I got to the Mother Brain, it took me
over 6 hours of playing that fight over and over and over again continuously to beat it, and even then, it was only partially due to strategy. I think alot of it was luck. I've beat it since (as you do get a feel of what you must do to win after some time), but it's been so long since I played it I couldn't begin to tell you what that is
I will say that the ending was both shocking, and most enjoyable, though.
Hardest. RPG. Ever.