Not quite sure if anyone's mentioned these already, but there's a bunch of things I'd certainly love to see, and one of them my dad thought of which I thought was brilliant, so I'll start off with it:
Map maker: Hear me out, so things like the offices and cave sets are pretty random on their own, right? Good, but it'd be even better if we could make our own maps based on these sets (Abiding with plot size limits), for our missions, rather than sticking with the ones that are already laid out for us. It feels like there's a lot of creative potential here that's being left untapped or inaccessible, or perhaps even being neglected. Lots of potential to make AE missions so much more interesting, and can even bring more spawnpoints for NPCs and add to the story and things like that
More dialogue slots, especially when certain things happen: Right now, they're pretty basic, very similar to a radio mission or a generic mission (Not a story arc mission), again, more potential that could be put to good use, but instead is being wasted, the mission creation could be a whole lot more elaborate here, and I guess as to not overwhelm people, these extras should be sorted into a whole "Advanced mode" type thing
Cutscene creation/NPC banter: There should be a way to make cutscenes like most story arc missions have got, and a way to have banter between NPCs, like in the Finale for the Shining Stars story arc (I believe this is also present in the Hearts of Darkness arc as well, again, a lot of creativity that can be leveraged here, but isn't
In-mission dialog boxes: I think it's pretty self-explanatory here, but in case an explanation is needed, we've all seen them, you go up to an object/person in the mission map, and the same dialog you needed to get the mission in the first place pops up, and you can have multiple choices of dialogue or just a single one, depending on the construction, and certain things can happen based on logic the user defines
Full unlock of character creation: The same pieces we have in the character creator, with customization palettes and all that, so like the parts for Arachnos Soldiers and Fortunatas and all that should become accessible dependent on chosen powerset
Unlock all powersets/archetypes: Things like Arachnos Soldier, Warshade, so forth, these aren't present currently and they really should be, as I have a character (Arbiter Jason) whose an Arachnos soldier, and my main is a Warshade, and these powersets don't exist at least unless you use the "Doppelganger" option, which doesn't exactly help here, as we may want to create custom characters with these powersets and have them with different colors of our choosing and so on
Methinks that about wraps it up, most likely I've forgotten a thing or more and just am not thinking about it...