Well, the main reason Marvel is so popular now is the MCU. Only about 10% of their revenue is actually from their comics. Which is bad for a comic company. So how can they get people to buy their comics/ watch their shows/ play their games? Throw something that looks like it's from their most popular creation on it. Like how everything Star Wars has Darth Vader apart of it. When something's so popular, a company's going to have to use it.
And their lack of Fantastic Four and X-Men recently is partly justified as well. They aren't in the MCU. If they become popular through comics or shows or games, and then a movie about them comes out, Marvel Studios isn't going to get that money. To Disney, using them in comic events and video games is no different from PlayStation advertising an XBox exclusive. Just advertising someone else's product.
I suggest you read Flashpoint first if you haven't already. Then read the Titans Hunt mini series from the New 52, since it establishes a few concepts that become important later on. You could also read the last few issues of the New 52 Superman series. After that read the Rebirth one-shot. The only important crossover I know of is The Button, a four issue crossover in The Flash and Batman. You could also read the Lazarus Contract, a crossover between Titans, Teen Titans, and Deathstroke, but I'm not sure how important it is. From there it depends what books you want to read. Most of them have been pretty good. The majority of them all had an issue 0 that set up the first story arc. All of them have the first few story arcs collected in graphic novels. I suggest reading The Flash and Titans, since they seem to be the ones that focus on the main Rebirth story arc. Oh, and you might want to read Watchmen.