Yes, Link lived and grew up in the church, but also lived a life in the city. He studied ancient sword techniques and went through physical training in his teen years. This will explain Link being able to wield a sword like a pro, and being able to do ninja flips around Hyrule.
Also, my art is coming along slower than I expected, but here is some art pulled out of Google images (so none of these are mine). I am just referencing these pics to try and communicate to everyone what I am visualizing for this weird future. By the way, some of these pics are huge, so I will just link to them instead of putting them in the post:
Lower City Alleys
Desert City?
More sophisticated Upper City (yes it is Star Wars)
Industrial Zone, in or near the Lower City
This one is actually real, Skyway
Another Skyway Idea
Center of the City (where the castle would be)
Maybe an Upper City bar?
Maybe the Castle itself?
Old Railway Systems in the Lower City?
Not a clue what this is, but it gave me more ideas for transit...
Another Center-of-the-City Idea
Construction in the Lower City
Those were my ideas on what the world looks like, now for my ideas on the new technologies... (by the way, anything above or below with a question mark means that I'm not sure if that is how I would like something to look)
A common Hoverbike (ignore the girl on the bike)
Desert Bike? (just slap on some off-road tires...)
Another Hoverbike (looks kinda like a horse huh?)
Hover Bus!
A possibility for Links new toy...
Well, my eyes hurt now from searching for just the right pictures. Hopefullt I get my own art up soon...
EDIT: Here is another one I found on Deviant Art:
Lower City Streets