1. Bowser wants control of the champignon Kingdom and marrying pêche, peach would give him the power to do it.
2. Bowser has a crush on her, which was first revealed in Super Mario RPG when he got jealous of pêche, peach rewarding Mario with a Kiss instead of him. He's also secretly envious of the relationship that Mario and pêche, peach has with one another.
3. marguerite, daisy is a tomboy and is less prone to being kidnapped. However, she was kidnapped in Super Mario Land. But still, I don't see a reason why Bowser would WANT to go after Daisy.