If you've just started playing it, congrats. Okay, here is are some nice tips I had learned ealier this month with my little brother.
1) When fighting Johnny Calamari, there is a sequence where you fight him alone. There IS a way to avoid it, but you need to be at a high level to do so. When you fight with him with the whole party, keep attacking Johnny and NOT the fish. I repeat, ATTACK Johhny and NOT the fish. After a while, maybe an hour of less, Johhny will dissolve and the fish will run off. There, you won with out getting into that single scenario.
2) When fighting Croco the first time with Mallow, get Mario to level 6 or so. 4 or 5 will do. Use Mario's JUMP (Or is you're that dedicated, Super Jump) attack with perfect timing. After 2 uses, use a Fire Ball. Croco's tail will be on fire and he'll be out for a turn. Use that time for Mallow to heal and Mario to use 1 MAYBE 2 Jumps. Croco will fall and you can progress.
3) When fighting Punchenello, Use Mallow's THUNDERBOLT attack, and use Geno and Mario's phycial attacks. Punchenello will fall.
I hope these tips work for you. Good Luck!