These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Supporters will argue that How Green Was My Valley is just as great a film as say, The Little Foxes (itself an underrated film) and better than the others, and was the most deserving title in the year of that competition aside from Kane, which was too controversial at the time to actually win.
Some Take a Third Option and dismiss the Oscars on the whole as a farce, and that it didn't matter if Kane or this film won, what matters is that both are great films.
Some irony is to be had in the fact that Orson Welles basically considered John Ford the best director ever. While Welles was probably perfectly understanding of Ford winning over him (Ford's The Grapes of Wrath was widely regarded as the best American movie for many years, until critics started giving Kane that merit), try justifying that to modern audiences.
How Green Was My Valley was highly innovative, its use of first person narration and the relation of that to the screen events went on to influence The Magnificent Ambersons.
Vindicated by History: The criticism that this movie has received over the years has toned down a lot in more recent times. While only a few people believe that it deserved to win, it now isn't uncommon to hear people call this a great movie.
The American critic, Andrew Sarris, called it the "best film to ever win an Oscar", he was a huge Ford fan(and a Kane fan as well).