Luigi can't go wrong with nearly ANY of his aerials, really. If you want to kill Petey Piranha without taking any damage or actually trying, just spam fireballs a far enough distance away and run whenever he jumps.
Also, his up-angled forward-smash works wonders against ground-based bosses, but only if you know their moves to the point where you can predict them perfectly. I usually just use rising tornado to down/back/up airs, and fall back down with a neutral air against Tabuu, or at least whenever I can get a hit in on him.
All in all, if you can predict well and spam B fast enough to tornado when hit away by Duon (he's very hard to fight as Luigi), you should be able to beat Boss Battles on Intense.
As for Ganondorf, just thunderstorm (auto-canceled down-air over and over for massive damage), and down-B away whenever something bad is about to happen. (Master/Crazy Hand about to grab you, as an example.) No matter how much you want to, do NOT go for a Warlock Punch; it's just not worth it.
In the air, you can up-air and back-air. Over, and over, and over again. But, throw in a down-air every chance you get for some much-needed damage. Besides that, just don't screw up, predict well, and hope to God that Porky dies as quickly as possible. Ganondorf was a pain; I don't really recommend him for Boss Battles on Intense.
For the record, I have beaten Boss Battles on Intense with these two, so don't just flat-out say it's impossible, because I'm living proof that it is. =P