I'll address a few of your points, though not in order:
Why would a court take this case? Because government enacted laws that gave individuals the ability to file suit against corporations. That's how the game works. Is it waste? That's a matter of opinion, but if there's a justiciable claim the court can't throw it out. And it didn't.
How is EA liable?: Let me try a different approach in explaining. Let's say we've worked together for years and I put a set of car keys on the table and tell you to "take it." You take the car keys and drive off with the car, but it's someone else's car. It wasn't your initial idea, but you still stole the car.
Is that a 100% match to the case here? No, but it illustrates the point that antitrust law is more interested in the deals that limit the free market than how they came to pass. It might not have been EA that came to the table first, but it's a serious possibility that its deals with the NFL/AFL/NCAA all around the same time amount to a violation of the law. I'm sure the court will consider how the exclusive license arrangement came to be, but that's only a piece of the puzzle.
Taking lower revenue: Contrary to popular belief, the USA is not a purely capitalist economy. If we were everyone would be able to take actions that would lead to the highest possible revenue. Screwing out the middle man? Sure. Slavery? Well, it helps the bottom line (not an antitrust issue, but you get my drift?). Antitrust law is meant to keep corporations from over reaching and disrupting the market in search of making the highest revenue.
Suing Budweiser/DirectTV/Nike/Reebok: I'm not sure where you're coming from here. A purchaser is able to buy other beer without an agreement with the NFL (Bud is an advertising sponsor, not a trademark licensee as far as I know). A viewer can watch most all NFL games on other networks or directly through the NFL's website. An athlete has plenty of options for apparel outside of Nike and Reebok (Under Armor, Adidas, etc.). If you're referring to NFL licensed apparel, read up on and pay attention to American Needle v. NFL (which is probably back in district court by now).
Anti trust law is a law of access, and as has been pointed out above posts the claimants and EA are going to make two different arguments. The claimants will say that someone wanting to purchase a football video game cannot do it unless it is produced by EA. EA has eliminated the competition's viability through its exclusive license agreements, and can set the price however it wants. On the other hand, EA will argue that someone wanting to purchase a video game (or even a game or disk based entertainment) has plenty of options outside of EA's licensed football games. Furthermore, EA's pricing is consistent with the rest of the video game market at $50-$60.
Hope that helps, or at least gives you a different perspective on the issues. There's still a lot up in the air in this case.