With the backgrounds added in, it's a toss up of 1 or 3 for me depending on which kind of style you like.
1 has more outlines so it gives more of a cel-shaded look, which may or may not be what you want. The style of the game will determine that. If you get rid of some of that black texture on everything, it may help make is smoother.
2 has a bit too much texture to me. I don't think it helps.
3 is more organic and smooth which I like. I did not pick 3 originally because it looked way too overexposed. I think it is improved now though I would still be careful not to make it too bright.
Now that you have more of "scene" than just a building sitting there by itself, you can continue to tweak and make better decisions. I always like to come back to things in a few days with fresh eyes. Also, feel free to try and ruin it and come up with happy accidents. I do this all the time, which is why I love digital. Make a backup and play with it until it breaks, and you may discover something you didn't think of.