Looking at the title, I totally thought this thread was going to suggest Mission Architect IOs with special bonuses that are only active in MA! 
I like the ideas suggested. Dunno how hard they might be to add to the interface though.
@PW - Police Woman (50 AR/dev blaster on Liberty)
TALOS - PW war journal - alternate contact tree using MA story arcs
=VICE= "Give me Liberty, or give me debt!"
I thought it was going to be about special MA enhancements too...
Winner of Players' Choice Best Villainous Arc 2010: Fear and Loathing on Striga; ID #350522
1. Arc or mission specific temp powers.
Since we've seen the tech can support conditional removal of temp powers, how about configurable granted temp powers capable of the following:
Use temp power on object objective - Like the redside arc where you use the scanner on the rikti pods.
Use temp power on enemy - Basically a flag on custom enemy, or standard enemies in groups that makes them invulnerable unless they've been hit with your temp power.
Note that these MA temp powers can not be used to deal damage, but simply function as a sort of "key" to complete an objective (scan box with special dimensional thingy, etc.) Or exploit a critical weakness in an otherwise invulnerable enemy (Use the special formula dart to make the invincible end boss defeatable.)
You could just select the power's animation from a dropdown of any of the avaliable "tool" temp powers ingame, or even a selection of animations from existing powers.
I think this could add a lot of options for immersion in specific story arcs.
2. New GR style in mission dialogues.
I like the "banter boxes" that accompany several of the new missions, flagging bosses blue until they're interacted with. Set these up as a new event type with a sub-field for stuff like objects, bosses, etc.
3. FAILURE
I hate how MA Missions can be failed, but the arc will automatically proceed anyway. There should be an option to either end the arc on failure, or recycle the mission. This would allow for the use of some complex mechanics in missions which require the players to actually COMPLETE the objectives (take down a fleeing boss, protect someone, etc.) to progress, so that failure doesn't break the narrative.
4. Choice/Memory
Several tip missions have an either/or success condition. I'd like to see this in the MA. Additionally, It'd be nice if we could get a forking OR style contact dialogue to choose multiple missions. I can think of multiple times I wanted to do a story which required certian choices to be made at the end, or even in the middle of an arc that I simply couldn't do effectively because of the lack of any options for player choices.
The new GR tech where events can remember simple boolean variables based on your choices woul be nice too. Just give the MA interfact four namable flags in the base properties of the mission, and allow the events to set these flags when completed, and be triggered to spawn on a "true" condition of these flags. This would definately help with tying together player choices across missions to enable optional objectives that mean something. (Optional rescue of hero complete sets my "Hero Rescue flag" True. Mission 2, I have an ally who's spawn condition is set to "Flag is true: Hero Rescue flag")