i htink you'll gain lot of power using 3D lines drawing instead of sprites ?
One trick can be to toggle on/off the grid also to gain some power?
for example only show the cubes where the player can go.

Even your texture of 1024*1024 can fit and be good like that, specially if it was for some mobile game.

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I've played DrakenSang Online :
They use 3D Tiles , they can put two or more layers of them in height.
And for texturing it seems they have some system that paint multitexture in top of all 3D Tiles, so this is not a simple texture per tile, but like some big multi texture paint for the level made of tiles ?
But i'm not sure.

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What will matter will be your characters, their attacks and special effects and all your 2D art, customizable things (characters equipment, powers etc ...)
The level is already good.

Will you make Final Fantasy tactics combat style : zoom on the map, or Fire Emblem like : 3D cinematic fight ?