Okay here are some of my comments to them.
1) I don't think Castle Town should surround Hyrule Castle. In none of the Zelda games Hyrule Castle has been ever surrounded by a town. In OOT the town was to the south, although the Castle was encased between the town and (more so) death mountain. In TP the town was in its entirity south of the Castle. And MC even had a bit of Hyrule field between the Castle and Hyrule Town. Besides if gets a bit hard to believe that the Royal Family doesn't see the slums from one of the towers when they are mostly surrounded by all sides.
2) The part of Death Valley south of the desert is a bit weird and probably pointless. In all the Zelda games that had a desert. The desert was surrounded by rock walls and there was only one entrance from a single area. It looks like some additional appendix just to justify Hyrule Field becoming Gerudo Desert.
3) In OOT and TP Zora's Domain is up on a mountain region. When Death Valley is at the foot of the mountain, it seems like Zora's Domain is on the level of Hyrule Field. And thus how would the water flow through River Valley. I always thought that River Valley was a river with waterfalls, that gradually flowed from Zora's Domain to Lake Hylia. You also said that Zora's Domain is underground, thus that would mean the water is flowing up?
4) There is a single off-shoot from river valley. Is that the only additional water way through Hyrule? For such a large large border with Hyrule Field and River Valley, there are no passages from one area to the other? Also Castle Town has only one passage to Hyrule Field, as the second one drops you in the river. In TP and MC there are more entrances/exits out of Castle Town. There are also no passages between Hyrule Field and the Valley of Death.
5) I'm not so fond of the cave passage connecting Hyrule Field and Goron Mountain. Just so that the player won't get into that area before it's time. There is nothing wrong with the player passing through a part of Death Valley a bit to get to Goron Mountain.
6) It is that you said that it is not at scale yet, because Castle Town and Lake Hylia are really small compared to the rest of the world. And Zora's domain is actually really large.