Shizuha
I feel like it would make more sense if she was destroying lands in some way, a la Reap and Sow. So I would do something like, "Sacrifice Shizuha, destroy target land. That land's controller searches their library for up to one basic land card and puts it into play tapped."
Minoriko
I feel like she should involve putting lands into play somehow, but seeing as how she matches with her spell, I'll let it slide.
Bumper Crop
I'd make it cost G. Since, you know, Dark Ritual.
Letty
Yeah, Letty isn't a god in any sense of the word. Definitely closer to an elemental. Or you could look at
the card that represents the exact race that she is, but thats kind of got block-style restrictions behind its creature types. I think Spirit or Elemental are the best ways to go. Incarnation is another possibility.
Renko
Okay. I'd probably at least make her a 2/2.
Kisume
Green? Really? Well...okay, I suppose she's fine.
Genji
I think 1/4 for 2G would be a more worthwhile setup. And I think you can give him flying, since, you know, his whole purpose for existing is that he's a flying turtle. Also another one where I'm curious as to why its green.
Yamame
I guess we'll have to wait and see what focus does.
Cave Spider's Nest
I'd probably opt for -1/-0 or -2/-0 rather than subtracting toughness only. Not only is only subtracting toughness...kind of weird, but I also don't think it makes much logical sense if this is supposed to be representative of a spider web. (Why do I keep trying to spell spider as 'spirer' @_@)
Scourge God
Cool.
Tiger Sign
Oh. I see how it is.
Flowery Sign
I...feel like this card needs to enchant a land rather than a creature. Paying three mana to make one of your creatures into a mana slave seems rather weak to me

Yuuka 2
"...you may reveal it and put it onto the battlefield tapped" is a better wording.
Also, drawing a card for yourself is generally restricted to minus effects on planeswalkers. Something to keep in mind if you plan on going ahead with the redesign.
If I was doing a redesign, I'd probably jump on the dreams aspect, making something messy like this:
+1: Exile target nonland permanent. Return it to play under its owner's control at the end of the turn.
-3: Put a nonland permanent from your hand into play. It gains haste. Return it to your hand at the end of the turn.
-9: You get an emblem with "During your upkeep, you may choose one: Exile target nonland permanent an opponent controls, or put a permanent from your hand into play. It gains haste."
I feel like its a bit strong, but its an idea for you to work with if you feel like a redesign.
Vengeful Flowering.
Hmm...I feel like this card is either going to fall really flat, or you'll be playing insects and it'll be way too strong. I might do something like "Enchanted creature gets +1/+0 for each mountain you control. Enchanted creature gets +0/+1 for each forest you control." A much more reliable, and much harder to abuse, effect, though in the end it'll probably have a significantly lower impact. I'd change the cost to 2RG for that effect.
And the second ability should be "Enchanted creature has 'T: This creature fights target creature.'"
Youki
Waiting for focus update....
Philosopher's Stone
I would take off the upkeep cost and the proliferate effect, to be completely honest.
Dragon
I'm just gonna say I hate annihilator with a burning passion and move on.
Dual Lands
Ho boy. I'm just going to talk about these all at once because yeah.
First, I'd change River Sanzu to Sanzu River, so that it matches with typical English word order. Secondly, I'd switch reaper to unblockable because reaper is just...not worth it. As far as why unblockable, I feel like blue's penchant for unblockableness and general trickery along with blacks penchant for fear and intimidate make it a technically appropriate ability. You might not like this considering Makai, but I'll get to that...right now.
I think Intimidate isn't worth it, considering the other possible abilities. So I'm going to recommend this: Remove Intimidate from Makai. Move Deathtouch from Netherworld to Makai. Give Netherworld Regenerate. To fix the overlap that causes, change Eientei to give First Strike (which is a much more technically appropriate ability, because two mana to give a creature immortal is a bit...:x).
As far as balance, I agree with JmLyan. They are a bit over the top as far as utility goes when it comes to lands, so I'd recommend one of the following:
-Make them add colourless, and add a new cycle of dual lands that are just plain dual lands.
-Force you to sacrifice one of the appropriate basic lands when they come into play.
Also, making them come into play untapped as long as you played spells of the appropriate colours...is virtually useless. In 90% of cases, this means you will have to play two spells just to get an untapped land. If you still have the mana to play spells after that, to make use of your now untapped land, I feel like you are probably doing something wrong. I feel like you might as well just make the lands come into play tapped and not clutter the card with meaningless effects.
Shrines
Reword the removal to say "Whenever [this card] untaps,...." That'll make it sound nicer. Also, I know it doesn't fit flavourwise, but I'd just make them all use faith counters instead of going half and half. It already doesn't make sense flavourwise for lands like the Palace of the Earth Spirits to be shrines, so I wouldn't add convoluting details like spirit counters just because.
Great Hakurei Barrier
Sounds fine. I might consider renaming it to Great Hakurei Border, just because that sounds nicer to me, but it's not a big deal.