I like bulgar and lentils, with sauted mushrooms and onions, garlic, thyme, lemon and paprika, couple splashes of soy sauce for the seasonings.
I first blanch the peppers, then stuff and use some kind of gravy (i like chickpea and mushroom) to pour all over, sprinkle with a blend of nutritional yeast and ground nuts, and bake just until bubbly. Im not the biggest fan of tomato sauce so it's my alternative.
I usually do it more casserole style, and cut the peppers in half and lay cut side up. I don't know why but it seems easier, and especially for reheating. Unless the peppers are very very small, but i got a dozen giant ones and that's what i did with them