I found PiT's final boss to be easy for the most part. The only phase I had trouble with was the first and that's when it got to use double attacks. Granted it was a long fight but I easily lasted to the end. Having free Mix Flowers when Luigi was low on health and large supplies of healing items helped too. I can't recall how difficult SS's final was since it has been a long time since I played it and I haven't actually played BIS.
Part of it was that I was underleveled, but about the first 5 times I got to the true final boss, it wiped me before I even got to attack. I mean, it got like... 5 attacks in each turn. Even the second time I played the game (wiping out every single enemy except for some in the desert and castle), it still could get about 3 attacks in per turn and was capable of destroyed everybody in a single turn if I wasn't careful.
SS's wasn't as difficult, in my opinion, but the fact that you start the fight with 1 HP means that if it's faster than you and can attack first... you either learned the attack patterns really fast, or you're screwed. Granted, the first phase of that fight only takes about 3 minutes (vs the 20 or so minutes in PiT), so dying there isn't too big of a loss.