To be fair to China, you can hardly say that the Manchu were 'supposed' to conquer them. It was incredibly bad fortune for the Chinese, or good fortune for the Manchu, depending on how you look at it. Ming was in the middle of what would be termed in game as a peasant war and they had essentially no money and no food due to famine so the Aisin Gioro just waltzed in there and took it because
they hated the Ming
The way to make Qing more possible would probably be to make some big famine event chain for Ming that gives them huge revolts and increases the cost of their troops substantially so they either have to disband, reduce maintenance (which would both help the Manchu conquer them) or find some other way to earn enough money to pay them (like trade or something, the player could do this)
P.S. I haven't ever played the Ming so I'm not sure if an event chain like this exists. If so it might need to be made more potent depending on how often the Manchu actually manage to conquer their way into China and whether that frequency is deemed acceptable