1. Bowser wants control of the 蘑菇 Kingdom and marrying 桃子 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 桃子 rewarding Mario with a 吻乐队（Kiss） instead of him. He's also secretly envious of the relationship that Mario and 桃子 has with one another.
3. 雏菊, 黛西 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.