I'm honestly fine with the differences in tone. Personally, I like how the Marvel and DC Cinematic Universes are going to be completely different because in the end, they are completely different sets of characters. Marvel's more colorful and playful tone matches with Marvel's set of characters that are more down to earth. DC's darker and realistic take matches with their set of characters that act more like a pantheon of gods and are superior beings to man.
The way the Walt Disney Company and Time Warner treat their respective properties is completely different though. Marvel Entertainment is a completely independent division within the Walt Disney Company and works in tandem with the ABC Television Group, Walt Disney Motion Pictures Group, and Disney Consumer Products. As a result we have a division within the Walt Disney Company that is completely dedicated to fully exploiting the potential of the Marvel Comics characters and it shows. DC Entertainment on the other hand is a mere subsidiary of Warner Bros. Entertainment which is just a part of the Time Warner machine. It doesn't get the attention that it needs and has to compete with other Warner Bros. properties like LEGO, Harry Potter, Hanna-Barbera, Looney Tunes, Lord of the Rings, etc. To make things worse, Time Warners divisions often compete with each other instead of working in tandem the way the Walt Disney Company's do. It's why Jeff Bewkes decided to spin off divisions such as AOL, Time Warner Cable, and Time Inc (stupidly I might add). The DC films also have a me-too sense of Warner Bros. playing catch up instead as well.