Marvel Games will not require games developers to hold to the existing Marvel continuity. Marvel Games creative director Bill Rosemann told IGN at DICE, "We want to give [developers] freedom to tell their story and we want to make it an original story." So, no the games will not be following the films or comics directly, though they will definitely be influenced by them.
Rosemann then went on to turn his instructions to devs into a food analogy, for some reason. "We want to give our partners…freedom to look at all of Marvel history and to pick from what interests them. It's a bit like we're saying, 'Hey you're the chef, you're going to make this meal. Here's all of the ingredients. You pick the ingredients that you like and make a new meal."
The four games currently in development for Marvel are Insomniac Games' Spider-Man for PS4, Guardians of the Galaxy – The Telltale Series, Marvel Vs. Capcom Infinite, and the Avengers Project by Square Enix.
Apparently the white emblem on Insomniac's Spider-Man was supposed to inform us that the games are not following directly in the footsteps of any pre-existing Marvel storylines. Which, sure, the hardcore Spider-Fans got. The rest of us, not so much.
One of the things I find most striking about this statement from Rosemann is that the Guardians series by Telltale is going seem "familiar to people who have seen the movie," and that Marvel Vs. Capcom Infinite will feature the film versions of the Marvel characters and none of the X-men. The most likely culprit for that are the licensing issues with Fox after the negotiations fell through. Still, the latest of the Lego Marvel titles has held to the film storylines exclusively. Gazillion, the developer of Marvel Heroes got in trouble with Marvel, possibly for holding a Fantastic Four event. But Avengers Academy is hosting an upcoming event is Monsters Unleashed which dovetails far more into the comics than the films. But Avengers Academy also avoids the X-Men.
And you may want to remember that Rosemann was brought in after several high profile layoffs in the Marvel Games sector over the failed Secret Wars game.
So, Marvel Games ignoring the comics is something of a pattern, though there are Mobile titles that do not follow this rule. Granted, there may be different licensing agreements for mobile titles and many of those pre-date the current Marvel Games leadership.