Sorry, came in a bit late here. Seems like you answered your own questions. A 12x12, regardless of height, doesn't allow much room for equipment. There are small pumps you can use that only require a few inches of water, you just need to shop around on it.

Honestly, thumbnails are the best bet for that small of a tank, darts may be small, but they like a lot of territory. Forget any terrestrial species, the tank is just too small.