Northern China was the first 'transmission point' for Eurasian technologies, and to an extent that gives them an edge over their southern counterparts. Chariots and bronze weaponry, for example, came to China via the overland corridor from Central Asia - and while there's an argument for the southeast developing their own indigenous casting techniques, the north would always possess a technological advantage of sorts which allowed for prodigious military expansion (i.e. Wu Ding and Di's campaigns, the Zhou conquest). Certainly you had places like Panlongcheng and Wucheng which seem to be analogous with Erligang/Shang culture, which suggests some sort of tributary/conquest process.
It's also possible that climactic changes were occurring at this time to which the south was simply less well-adjusted for. Intense campaigning during the late Shang and the beginning of the nomadic tradition in Mongolia suggests environmental pressures within the region that might have broken southern cultures. The relative isolation of Yangtze cultures due to terrain might have been a detriment to this end.
Lastly, one wonders if there is only room in China for one 'truly developed' civilization. Certainly Shang demand for tin and porcelain resulted in a pan-China 'network' (if not even greater control) with its heart in the Henan region. Similarly, the Zhou ritual system eventually became the dominant political system in China, with even 'barbarian' civilizations like Chu, Wu and Yue seeking to participate in it.
That said, certainly during the early Zhou period the proto-Chu were seen to be a dangerous foe to the Zhou, and during the early 9thC BC Chu managed to defeat and kill King Zhao of Zhou, thereby halting Zhou's southwards expansion. So it's not like the Yellow River cultures were dominant across China.