Bowser's main goal is to defeat Mario. He knows that if he kidnaps Princess Peach, Mario will do all he can to save her and might die in the process, or at least he can lead Mario into a trap.
1. Bowser wants control of the Mushroom Kingdom and marrying 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 Peach rewarding Mario with a kiss instead of him. He's also secretly envious of the relationship that Mario and Peach has with one another.
3. 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.