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, o at least he can lead Mario into a trap.
1. Bowser wants control of the seta Kingdom and marrying melocotón 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 melocotón rewarding Mario with a kiss instead of him. He's also secretly envious of the relationship that Mario and melocotón has with one another.
3. margarita 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.
i think bowser kidnaps melocotón and not margarita because melocotón is so girly and margarita is a tomboy like margarita has only been kidnapped in one mario game