Obviously another time-heavy addition, but it would be great if at least the engine itself allowed for static tiles to be replaced with animated ones in the future (....hey, they did it with Minecraft afterall!). A little bit of movement would be nice.
I'm hoping, too, that eventually someone mods this so that we have some nice optical effects (glows, flares, fog, etc). I'm all for the clean graphic style, but I also find that this look can still work well with 'real' optical effects.