My wife and I have been playing a lot of Marvel Crisis Protocol during the pandemic, and I have to say, most of the time, we don't really play by the scenario rules. We follow the rules for gameplay, which are quite well-explained and don't have a lot of room for modification without throwing off balance. What we do tend to do, however, is modify the scenario rules a bit to make the game a bit faster and often an interesting way to try highlight particular characters. Definitely don't try this in a tournament setting, though. Here are some of the variant rules we've used in casual gameplay at home:
Double Victory Points
This sticks pretty close to normal play, but helps speed up the game when you don't have a lot of time to play. We've played games this way that have taken about an hour from character selection to final victory point tally. Doing this shortens the game, and often makes it about characters with greater mobility grabbing extraction objectives and moving them around to bank points while the slower characters take their time, moving in to defend objectives and grab the points needed to finish off the game.
We do this a lot, to be honest. Especially when we get new characters and want to try out their abilities in combat. Fighting is a big part of the game, and this is just a style play where each side beats each other up. Basically, we just pick a high threat level around 20 so that we can each pick five characters (or possibly more), with 2 victory points awarded per character dazed or KO'd. On top of this, we even
allow special victory point bonuses such as Killmonger's Usurp the Throne card so that he has a chance to get extra victory points from kills--though we haven't tried this with Thanos' leadership ability that allows the Black Order extra victory points for KOs. Since Hulk can't be dazed, we give double when he is KO'd. This is a fun way to play, and it really highlights the abilities of characters who are great in combat. Faster characters that can run and hide also make the game interesting.
Sometimes, we don't want to bother with 2 objectives, and we just pick one. When you've only got one objective, it's often a good idea to combine this play style with the Battle Royale or Double Victory Points play styles listed above to keep the game to a reasonable length with the 16 victory point limit still attainable. If you've got some nice terrain, such as 3D printed buildings, playing "secure" missions really makes the terrain the star of the show. You can set up your your board so that you can place your objective tokens on buildings and have your characters fight for control of parts of the board. For "extraction" threats, the Wakandan herb scenario stands very well on its own as a playable scenario. The "Worthy" scenario, which gives players control of Asgardian hammers is a great scenario to combine with a Battle-Royale-type game by giving characters some extra dice to daze and KO opponents.
This is a bit ambitious, and we haven't tried it yet, but we plan to in the future--especially once we have the terrain and minis to pull it off. Once we're able to do so, we're definitely try to homebrew our own Secret Wars, Age of Apocalypse, Civil War, Seige, The Contest, XvA, and other scenarios based on our favorite comic stories. We can't wait to have the minis to make this possible, and with any luck Atomic Mass Games will provide us with scenario rules that represent these classic Marvel comics stories before we even have to make up our own!