An underground mine cart system that leads all over Hyrule. Just imagine; an Indiana Jones-style mine cart chase with Link fighting off Moblins that are in another cart.

Or maybe Link having a dragon or something to ride on, other than Epona. Maybe the dragon could be used to cross large gaps Epona couldn't jump.

Heck, why not some sort of magical jetpack? Wait, that'd be too much like Mario Sunshine...

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I am not going to be on this site for about a month (not that it matters much) until I get Spirit Tracks and beat it. (I don't want the plot spoiled, after all.) But I'll be back!