Adding to my list...
Fully Scriptable UI
Popmenus are nice, but limited. Replace the current in-game 2-D interface with a Lua scripted UI and backend API. Allow players to extend, compose, or replace these UIs with custom, user-created addons.
Replace Immersion-Breaking "Stores" with Something Else
Having NPC contacts, especially heroic/villainous contacs, offer to sell you things on the side -- while convenient -- is very immersion breaking. It's like Eagle Eye or Glacia are heroes down on their luck, reduced to trying to sell me fake Rolex watches. Or that every NPC contact is desperate to sell me some Amway rubbish or a gaudy LuLaRoe print.
A small improvement would be to replace "Ask about the store" with an NPC-specific, cannon-appropriate call to action.
Another would be to replace influence-based NPC "stores" with a resource economy; bonus this provides an alternative use for salvage. So it feels less like the person is a stand-in for a store, and more like someone who's helping me out by crafting something useful after I bring them the raw materials. Sure, some contacts would naturally be peddling something in game; those would remain influence based stores (though a better call to action would be nice).
An alternative way to address the convenience of having "stores" everywhere would be to redesign one of the city zones to have a market district with every origin store, Icon, Wentworth's/black-market all in the same few blocks right next to the transit. Talos Island for heroes is a great candidate as it's already accessible from Ouroboros. Perhaps this is a good use for Kallisti Warf at higher levels (if made accessible from Ouro as well).
The contacts who -- after getting in their good graces -- offer you enhancements, those enhancements are rarely beneficial, making it a pointless achievement. If instead they were unique or beneficial beyond what you could get otherwise, there would be a purpose to improving your reputation with certain contacts. This seems to be the original intent of the system, but it isn't successfully realized.
There's a spectrum between convenience and making it feel like you're doing MMO chores. The pendulum has swung too far to the convenience side. It's eliminated a worthwhile activity I could be doing in the game.
Gangs and other immersion breaking mobs
The random clusters of mobs in the streets of a city filled with heroes feels ridiculous to me. It's one part West Side Story, one part absurdist dystopia. While it's fun to imagine the residents of Peregrine Island have become so accustomed to weird shit happening all the time, that they just blissfully walk down the street past clusters of Nemsis or Rikti just chilling in a parking lot, it just feels silly and immersion breaking when you stop to think. With some good writing this could work for Peregrine, but almost all the zones from Atlas Park onward suffer from this. Even the zones intended to be overrun by mobs it feels silly with factions haphazardly thrown on the map with no particular in-game reason to be where they are or even in that zone.
There has to be a better way to satisfying the competing needs of having mobs to farm/street-sweep, not having to travel too far out of one's way, and preserving immersion. Successful, well maintained parts of a city zone wouldn't have random thugs in it. Neglected and industrial maybe so. Areas overrun with baddies that are barely kept at bay, yes. There should be a logical transition from one type of area to another.
Part of the problem is the linear, flat feel of most city zones. With WoW, Blizzard designers make excellent use of vertical terrain to create horizons where transitions from safe zones to combat zones make sense in the game world. The world of CoH needs to be less Manhattan and more San Francisco in terms of its terrain. Drop the war walls, eliminate loading screens, shrink some zones, and leverage terrain variations to make the transition from bustling city to thug infested backwoods make sense.
The parking structure under the PPD HQ in Kings Row is overrun with Skulls. The parking lot would a) be filled with police vehicles (it isn't) and b) have cops coming and going so frequently that crime would almost never happen. This lack of intentional design is a recurring theme throughout the game.
Add Undo to Enhancement Management
Until I leave the enhancement management screen, there's no reason anything I do -- from filling a slot, deleting an enhancement, to combining -- should be a permanent decision until I commit my changes by "Saving" or "Committing" and leaving the management UI. The "are you sure" dialog boxes aren't the solution; everyone immediately checks the box to make them go away. Confirmation dialogs are always a sign of failed UX; usually an indicator that you didn't implement some form of undo.
On a similar front, irreversible operations like attuning a +N enhancement are terrible traps that frustrate and cost the player significant amounts of influence and time. Undo as I described would do a lot to solve this.
Flight Poses & Travel Power Improvements
Fly poses should either be a sticky configuration instead of emotes, or the fly emote system needs a rework. You can search google/reddit for the kludges players are required to use in order to have a custom fly pose.
As mentioned in other posts, whether it's through a pose system or by making travel special effects more customizable, there should be more options: fly upright, on a hover board, in a personal chopper, running on a magical tiled walkway that appears in front of every footstep, etc.. I don't want my arcane themed character flying around like superman (and the purchasable flying carpet cannot be boosted and turns off toggles).
Minimal FX Option for Everything
Outside of PvP I should be able to disable effects on almost every power, certainly every toggle and travel power.
Color Options for Everything
Most powers allow you to choose Bright/Dark color palettes as an option. Those which don't, should. Those which do, but ignore one or both of primary/secondary color should be made to honor them.
Lethal Falling Damage
Lethal falling damage for NPCs/mobs. If I'm fighting a super, they should take damage. If I just launched a prisoner off of the Zig, they should be dead/incapped.
This should be true for some heroes, too. Maybe certain secondaries make you immune (e.g. Invul, Super Jump), but it's appropriate even in comic books for falls to be lethal or take a hero out (War Machine's fall in Civil War, for instance). If you cannot fly/hover before landing from a high enough fall, this should take you out.