I'm not going to speculate on what they're going to do. Nothing really is extremly obvious. The elevated walkway seems to make the most sense. Especially if they're planning on developing further parking across Habor, and even potentially that third park in the Toy Story lot...
Even if Disney chooses not do anything with it, they have an inherent interest in owning property in the Resort District. They can make sure development happens in a way that suits their purposes.
Here's some pictures...
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Above is the Transportation/Central Plaza where just across the street you'll see the hotel they bought (look for red pin). Harbor is lined with all sorts of hotels like there new one. There's very little space to do anything big. That's what makes the land bridge interesting to me.
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(Look above) Just south is the Pumba lot (Purple Pin). Building a bridge over Harbor means that guests could easily make their way from the Pumba lot while walking, and as an added benefit all those hotel guests can walk over it too. Start the day right. As I understand it, Harbor serves as an important artery for commuters in the area. Vastly reducing pedestrians would be great for traffic flow into the Resort District.
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(Look above) Finally, this is the hotel relative to the Toy Story Parking Lot (Purple Pin) most likely spot for future parks and maybe even hotels. Needless to say it's not very close to the the recent hotel purchase (Red Pin). That's what makes it unlikely that it will be anything related to a 3rd park. Now having walking access to and from traditional Disneyland and the 3rd park makes sense. Another reason the bridge is compelling.
Just praying they don't waste the park on Marvel.