I wonder if we can make a low-budget one which tells a good story and which uses miniatures.
Yes, I'm pretty sure you can. The trick is to make one without just a good enough story, but incredible cinematography and effects (be it practical or digital) and overall look and acting and sound, etc that competes or surpasses the big guys. That's where it gets hard... but still probably doable with a lot of time and elbow grease.