A native Chinese dynasty like the Shun is the most likely result, though there exists potential for Mongols or another steppe people to do what the Manchu did in OTL. Then, it will be the policies of the new dynasty that will have the largest effect. I believe that the Qing had an even greater suppressive influence on Chinese technological and economic development than the late Ming.
Manchu disunity would have effects on Mongolia and Korea as well, which might be worth keeping in mind.