Video game villains rarely have very developed motivations, although when a series uses a villain over and over you get some more sense of what makes them tick. Bowser Koopa, while hardly the most threatening bad guy in the video game world, does show up quite a bit. Several years ago, Drew Mackie speculated on reasons why Bowser kept kidnapping the Princess over and over again. The idea that he’s in love with her seems to have started in the Nintendo 64 era, but it’s not entirely clear that this wasn’t supposed to have been the case all along.
The Super Mario Adventures comic based on Super Mario World had the Koopa King wanting to marry the Princess years before it was ever mentioned in a game. There was also an episode of the Super Mario Bros. Super Show where he wanted to marry her, although it seemed to be more for political power than because he was in love with her. There wasn’t much consistency in the cartoons, but most of the time Bowser was after a material reward, either control of a country or valuable stuff he could steal, if not both. The kidnapping was usually an attempt to strong-arm the Princess into giving control of her kingdom to him, although he did occasionally show interest in her beyond that. Hey, maybe for Koopas kidnapping is an acceptable form of courtship.
Actually, the instruction manual for the original Super Mario Bros. said that he had captured the Princess because she was the only one who could break the spell that had turned her people into blocks. I’m not sure why she couldn’t do that from inside the castle, but maybe she was in a magic-proof cell. In Super Mario Bros. 3, Bowser’s main goal seems to have been a land grab, with each of his children taking over a different kingdom by transforming its king. It’s only after Mario restores all of the kings that Bowser turns to his old hobby of kidnapping (well, unless you warp). In Super Mario World he kidnaps the Princess and his kids steal a bunch of Yoshi eggs.
What’s not clear is why he’s in Dinosaur Land in the first place, when Mario, Luigi, and Peach are there for a vacation. Did he know they were coming and ambush them there, or was it a coincidence that they arrived there around the same time? King Koopa apparently already had some territorial claims in Dinosaur Land, since we learn in Yoshi’s Island that he spent time in a castle there as a baby, and there’s an island there shaped like his head.
As this Cracked article points out, the sunken ghost ship that you have to make your way through to raise the Valley of Bowser from the water resembles one of the airships from the previous game, and is even specifically identified as one in some media.
Maybe the Koopa family’s ship broke down over Dinosaur Land, so they decided to make the best of things and conquer the place. The football team had also somehow ended up there, which is why the Chargin’ Chucks are some of Bowser’s top troops in the game. I’ll admit that the Super Mario World cartoon was influential on this idea, since the SMB3 cartoon showed the Koopas having access to some pretty advanced technology, while the SMW one shows them stuck using what they can find in the stone age society. Perhaps they hadn’t yet figured out how to get back to their homeland. Since then, Bowser has largely stuck to kidnapping Peach, although sometimes he kidnaps someone else, or has a plan in addition to the kidnapping.