@pkourany - I feel your pain. I have pretty well isolated the issues with mine (Basic) to the pin and header connections for the MBus connecting the core (main) board with the sub-boards and base. After posting earlier, I actually took my bottom plate off and pulled the 850mah battery holder to check a few things related to some secondary circuits I am designing. I had fits getting everything to work again.
The stacking idea is a nice approach, but as an ME what I am seeing are tolerance issues with engagement of the male pins into the female sockets. I think there is a luck of the draw thing going on. There are mechanical tolerances on the pins and headers which will have variations from set to set. The same applies for the housings. Some of us just seem to have those at the extremes and end up with dicey header connections. The other compounding challenge tied to the pins seating is that all the male pin ends are tapered to help guide into the sockets - makes getting solid contact in the header all the more a variable thing.
I am in the process of looking at other ways to skin that particular cat and will let you know if I come up with something. Of course, one thing that helps me is that I have a different form factor in mind for how I want to integrate things and may be able to avoid. It's tough coming up with a stacking header system in such a small form factor as the M5Stack.
I think you will really like the device once you get past the issues you are having like some of the rest of us. It really is a nice setup and I am hoping that some of the growing pains and feedback work into better solutions for the next editions. Sucks a bit dropping the coin for one only to have to fuss with it to get some basic things to work.
JimiT noted that the manual states you may need to hold the power (red) butting in while flashing. Haven't tried that myself yet but that may be a short term option. If you get a clearer image of the board so I can read the SOIC chips, I'd help identify the ground points.