Personally the only thing I felt looked at all flat was the ground textures (sorry if this worries you at all), but I think the easy solution to that would be to adjust the grass and dirt ground (top of the ground texture) so that the flatness of the ground doesn’t translate to the surface.

If you look at these:
http://s.uvlist.net/l/y2005/9/8276.jpg
http://buysomeindiegames.files.wordpress.com/2012/05/projectblacksun.jpg?w=593&h=304
http://img.brothersoft.com/screenshots/softimage/c/castlevania_-_aria_of_sorrow-171040-2.jpeg
http://www.pocketgamer.co.uk/FCKEditorFiles//friday-fiver-dark-incursion.jpg
http://i297.photobucket.com/albums/mm224/silent_snake18/symphony_1.jpg

you’ll notice that they use lighting and other tricks to help enhance the surface of the ground to help give a sense of texture and depth with only a few pixels.
I recognize this is a lot harder to do with transitional effects between tile types, and what not… that’s why I would suggest using the grass layer to accomplish this and not worry about it on every tile.

Cheers!