I could be wrong, but it sounds like you're just kinda of winging it with the dungeon. Like you're making it as you go; without a plan.
I do like where this could go. With all the plants and water, I like the feel. There are a few tiling errors as Sinkin said, but I'm sure you plan on fixing those up.
I actually like having the big trees inside there. Nice touch.
Still though, I suggest that you plan out the whole dungeon by mapping it out. Just sketch out the rooms and some rough ideas of how it will all hook together. Among other things, it will seriously improve the complexity of your dungeons.
Some ideas about those holes:
- Maybe Deku Link is short enough to travel through them?
- If Deku Link can spit nuts, then maybe you have to spit nuts into/through them?
- Change water flow to go through the holes (ones that make a tunnel) to flip switches or to fill a pit in order to cross it (if Link can't swim, make a floating piece of bark rise with the water. And Deku Link would be light enough to hop on it ^_^)
- The classic rat could dash in and out of the holes and you'd have to plug all the holes but one in order to kill it. Of course the rat would be carrying a needed key or something.
Or were you asking for ideas? LOL, well there's some thoughts just the same.
Did I mention how much I like the feel?
Summary: Fix up the tiling errors, maybe make the water not so rough (if you have edges for it?), and plan the dungeon a bit more before going any further with it.
EDIT:
One more thing. It seems like you've got quite a story there. But why ruin it for everyone? Unless it was necessary to tell us that..? Maybe it's just me, but letting an exciting story unfold with all kinds of plot twists etc; that's half the fun! ^_^