There's some brilliant foreshadowing through some of the missions as the game continues. For instance, the strange device that drew the large creatures to it in mission 1.6? With Latverian manufacturing? A prototype for the machine Doom used in Mission 12 to drive his rivals against each other.
When Spec Ops 11 started, the Chess Set, which was introduced Spec Ops 2 for Emma Frost, was re-released. Why was this? Daimon Helstrom was the White King of the Hellfire club.
Players were expecting a Wolverine Spec Op to tie-in with The Wolverine after the successful adaptation of Iron Man 3 in a past Spec Op. By the time of the Wolverine movie, the game released a pseudo-sequel Spec Op for the Dark Is Not Evil heroes instead. Why? 20th Century Fox still owns the movie licenses of the X-Men characters, and this is still an MCU promotional game. The plots of the movies are Fox's intellectual property. And besides, why would Marvel waste time promoting a rival studio's movies?
Considering that command "Rest" restores the similar amount of stamina as the Stamina Boost Pack I one may question usefulness of this item. You start to value this things (not much, but still) once you learn that you get nice bonus points for completing the battle without a single rest.
Doom starts out with higher than average health, has more than four moves and goes twice a turn. Now of course, this is to compensate for not being able to team-up with other heroes. But if you think about it, he's still a Boss-type character and the agent is his minion.
The heroes go apeshit when you recruit Doctor Doom, and absolutely refuse to work with you as long as he's on your team. Fair enough, but how does that explain why some of the bloodthirsty villains on your side (such as Juggernaut, Satana and especially Sabretooth) refuse to work with him also? Balancing aside, it can't be because of Even Evil Has Standards.
It probably has more to do with Doom's massive ego refusing to work with anyone else rather than everyone else refusing to work with him. Even the Agent is kind of just tagging along to keep an eye on him.
Hydra Exoskeletons cannot be affected by psychic attacks as they are "Mindless". This means there is nobody piloting them, so why are they called "Exoskeletons" instead of Drones or something more appropriate?
Maybe the pilots have cybernetic implants that help them operate the suit. The implants stop the pilot from psychic attacks is a bonus for HYDRA (and AIM for that matter)
Season one, chapter 12, 5º mission. Magneto fights against Red Skull. Red Skull says: "There are certain truths that do not change, nicht wahr? One of them is that you and your kind are an aberration. The dawning world has no need of you, no use for you, no desire to suffer your presence". Of course, he's talking about mutants... but, considering that he is a resurrected nazi leader, and Magneto an Holocaust survivor, it's hard not to find second meanings in that dialogue.
The Incursions in Season Two, and to a lesser degree the PvP seasons. In Jonathan Hickman's Avengers, the only way to stop an incursion is to destroy the entire world. The player character is a genocidal murderer?