I've thought the same myself. I loved Minecraft the first time I laid eyes on it years ago. I thought it was something neat and interesting and not once did I go "man the graphics suck why isn't this like AAA games visual wise?". I like that Starbound is a 2D pixel version of Minecraft/Terraria, it being in 3D would have made it look more like Minecraft and we've all seen that song and dance played by a good numebr that tried to emulate MC's success and looks.
Actually, I think a 3D space Minecraft could work pretty well if done right. If it had mechanics like Starbound, I think it could be pretty cool. Though SB as it is is pretty great too.