The Imperfect Missions (where you play as an Imperfect character [or evil Marvel character] to defeat a Marvel character) can be done in any order and for both Any% and All Character Missions, 6/9 of these missions must be completed.

Here's my ideal order of doing these missions
1) Defeating The Thing as Fault Zone (Thing is stronger but this mission should be ok for you. Be prepared for Thing catching cars you throw at him and him lifting cars/the van to throw at you)
2) Defeating Daredevil as Solara (Can quickly kill Daredevil by luring him into the fire pit at the top left of the arena)
3) Defeating Venom as Hazmat (Just swing over the pit and Venom will kill himself)
4) Defeating Spider-Man as Johnny Ohm (You can get Spidey to kill himself by flying around Daily Bugle and he will ring himself out. This can be tricky though. It's best if you first get onto the Daily Bugle letters to gain some decent height and avoid ringing yourself out)
5) Defeating Human Torch as evil Spider-Man (This mission can be tricky. Try using Spider-Man's extra strength and super grab to sling heavy items towards you)
6) Defeating Wolverine as Brigade (With the exception of the super block, Wolverine isn't much of an issue. The fastest way to defeat Wolverine is to hit him with lamp posts and throw them at him when he's at a distance)

Here are the missions I don't do and why
- Defeating Elektra as The Wink - This mission is genuinely quite difficult. Elektra is much more of a pain in this mission than expected and The Wink is not a strong character. (Also slow menuing as 2 inputs are required to select this mission i.e. 2 right or 2 left)
- Storm as evil Wolverine - I don't think this mission is particularly hard but is quite long as Wolverine has no long-range attack other than throwing items and he can only throw small objects which deal less damage. Also requires 1 additional input
- Iron Man as Niles Van Roekel - Iron Man is a very difficult character to fight and while Niles Van Roekel is also a strong character with good moves, it can still be difficult and/or long to beat Iron Man. Also you only get 1 opportunity to do this mission and its better to choose the Brigade vs Wolverine mission over this because it's much easier

Reasons why my order is the most ideal
- One reason why I think my order is ideal is for the purposes of menuing. If you do these missions in this order, you don't have to move to the right of left to select missions and can just mash the button to start the mission. Saves minor time but still significant. If you do the missions in this order, the only menuing you need to do is to select the imperfect mission as Brigade against Wolverine, and the first 2 Magneto missions which each requires 1 input (and all the missions for Wolverine, Elektra and Storm)
- Leaving the Brigade mission to last which is arguably the easiest of the Imperfect missions which removes some stress late in the run.
- The missions I choose are easier and faster than the missions I choose not to do. Missions 5 on my list can still give you some problems but is still better imo. The rest should be fine most of the time.

Of course some runners have different preferences. If you think certain missions are harder than others, you can do these missions in a different order but this is the order I recommend. If you can think of a reason why my mission order isn't the most ideal one, please post why you think it's better to do certain missions earlier/later than others

I'm currently practicing the Rage of the Beast mission (where you kill Storm as evil Wolverine) and it actually seems pretty fast consistently for me. I think this could replace mission 5 in my mission list.

Really the only mission I'd say to avoid for sure is the mission where you defeat Elektra as The Wink