I have used the Helix mod to remove the 2D shaders making Shogun 2 unplayable in 3D. I can finally play this game!
total war shogun 2.zip
To install: Simply unzip to the folder where the Shogun2.exe file is. Mine is found: C:\Steam\steamapps\common\total war shogun 2
To uninstall: remove the dxd9.dll and shaderoverride folder.
Required graphics settings: DX9 mode, Shadows off.
The battle phases
Both land and sea have had all the dodgy effects removed. So much so I would call it 3D Ready if it weren't for the 2D mouse. Personally 2D mouses concern me less in RTS where they would be a game breaker in an FPS or 3rd person game. I guess this is because you can move them and you can still accurately aim between the 'two' cursers...
You do lose flaming buildings and ships but the be building do look like they are smouldering; the ships just have a heat wave effect around them now though. Flaming arrows are fine.
The campaign map
I have removed: roads, rivers, province borders, province zones and unit range zones have been removed. This isn't as bad as it sounds! Roads and rivers are cosmetic (I didn't realise they had gone and the bridges remain as visual clues), the minimap still shows the province zones and borders and holding right mouse button previews the selected path of the unit including range and turns required!
The only issue remaining on the campaign map are the town names which are 2D. This would do my head in during battles but I don't mind them on the campaign map for some reason... Also the abovementioned unit path preview is borked but this is completely minor.
For those who want the campaign map left alone and are happy to toggle 2D for these sections
Inside both pixel and vertex shader folders is a folder called Basic. Remove and replace all the shaders with the ones in the folders. (I have simply removed the shaders relating to the campaign map.)