I don't use my brain? Seriously, I'm taking that as an insult, because I don't think I deserve to be called stupid because I don't see what you clearly do.

Putting The Minish Cap first, note this: there was seveal huge wars at least a decade before Ocarina of Time that ingulfed the entire land, so of course things would have changed.

You really don't use your brain do you!

Play Twilight Princess before you expect to see Kakariko Village in The Minish Cap when it is regarded as first - Kakariko Village was hidden and the Sheikah were hiding there for all those years, so of course there will be no sign of them in The Minish Cap!

The Death Mountain Kakariko wouldn't be around in The Minish Cap - except the Hidden Village would be, well, hidden, obviously - because it was fairly new during Ocarina of Time, too new to have existed during The Minish Cap. The Sheikah, as Twilight Princess proved, were hidden in Hidden Village for all those years, only showing themselves when the wars broke out.