From what I've read it seems both countries were approaching the "opening to the west" in similar fashion although China appears more reluctant. Both isolated the majority of the western trading to single ports/cities (thinking Shanghai concessions and Kobe's quarters), but over the years it seems the movies, fiction etc I consume always seem to show Japan in a much more positive light.
Did the Opium War and Boxer Revolution (list goes on) create a shoddy foundation with China early, from which we've never recovered or have the end of WW2 + Korea + Cold War created a bias in how these countries are portrayed by the west?
What kind of bias are you talking about? It's difficult to answer this question without some examples. But, I can say West-Chinese relations at that time were without a doubt far more antagonistic and dysfunctional that West-Japanese relations.
The various conflicts of the 19th century left behind a set of long-standing disputes that were never really resolved until the 1930s and 40s, such as the indemnities demanded from China by the foreign powers after their various wars (these crippled the Chinese government well into the early years of the republic, despite China's efforts to renegotiate them), the legal status of foreigners in China (who were immune to Chinese law), the trading rights of foreign merchants, and the status of the foreign concessions (the miniature colonies established in Chinese cities). Relations with the West, as well as China's internal politics, were dominated by these disputes well into the Republican era.
I don't believe Japan had any comparable issues in its relations with the West in the first few decades of the 20th century (apart from its war with Russia).