Okay, here is a list of what i think should be changed, added, removed, etc.:

1) Abort button for deploying. Quite often i find myself clicking deploy only to realize that i forgot something. Deploy should take a minimum of 3 seconds, during which you would have the option to abort it.

2) Mission UI: When you complete a mission inside a station through delivery, there should be no popups about completeion, unless it actually has something important to tell you: like you are missing some mission items, or objectives, etc..
2/a) Messageboxes are generally poor UI design. You should find someplace else for that information and forgo using boxes that are also associated with critical error messages. You do no really have to show mission objectives in such an into-your-face aggressive manner. After all, there is an assignment log that you can open and use to keep track of assignment progress

3) Assignment log: it should be a tree style list showing all assignments with expandable objectives, so you can have a quick overview of all the assignments you have taken and their progress, while also get in-depth information about the one you do at any given moment.

4) When finishing assignments, the reward items you receive are not stacked against those already in your storage space. This results in N stacks of 35 ammo for each mission you did. Minor issue really, but it should also be fairly trivial to fix.

5) We should have the ability to move items between bot equip screen, private storage, bot cargo, corp stores / folders. Its fairly annoying when i try to equip my bot from corp store, only to realize i have to move the item into my own store first, or bot cargo for it to work.

6) Market: im not even sure where to begin. The cheap way would be: take a look at EVE's market and aim to have at least half the features that one has What would be really useful:
6/a) Market history: see a graph of what happened to an item over time: hourly/daily/weekly bar chart showing min/max trading price and trade volume for the item.
6/b) Clarify the UI a little: Place order button should be moved to a less prominent position as its wording/position now suggests that it actually initiates trade, while in reality all it does is open up more options. It should be renamed to custom order or something along those lines. I was afraid to press it at first, thinking that it would cause me to sell my stuff at the ridiculous prices offered by some Yes i know its ridiculous, but it actually happened and is a good illustration on how bad wording / button position can mislead people.

7) Corp management UI: Lots of things there.
7/A) Corp Storage: The close button for corp storages has to go somewhere else. I think i actually clicked that once right after creating a storage unit, to close the window. Not sure which genius did put a button with the caption 'close xxx' to the top right of the window, but it is a sure way to cause headache. Also since i got no confirmation dialog before losing my storage unit, there is two possibilities:
7/A/a) In case the close storage button has no confirmation before closing the storage unit, add one quickly.
7/A/b) In case it has a confirmation, then there is a weird but, in which you 'lose' a storage unit right after opening it...
7/A/c) The corp storage history could use a search/filter function to filter on specific items or specific people and also to filter between a given time frame.

7/B) Member management: when trying to set storage access rights for people, the list keeps refreshing itself, which would not be a problem, but whenever such a refresh happens, the boxes you ticked to set rights (thats the 8 boxes, 4 for in, 4 for out) get reset to defaults. Also once you set delegate right on someone, you cannot remove it, which is just bad practice.
7/B/a) There also needs to be some sort of help/info about the various rights either as links to the ingame help, or as a short tooltip, as for the newbie CEO, most of the titles mean nothing.

7/C) Storage again.. i understand how you can have multiple storage units and those go into the big corp storage window, but this also means that you have to go through one more window to get to the actual storage space. Also dislike the 4 levels of storage access.. For small groups, 1 levels with maybe a protected sotrage area is enough. Those groups do not need extra windows to get their little sotrage space. For large groups however, the 4 levels are a joke. Sure you can work around the limitations or try to work out a system inside this, but lets face it.. its just an arbitrary limitation.
7/C/a) Suggestion: Have just one corp storage and use the folder system you already have, which is a lot nicer. You should be able to set up any number of groups / divisions inside your corp and then grant access to folders based on these groups and the available rights: view/take/add. The storage system could be reworked to impose a limit based on capacity, so say the base storage unit can hold 50U, and you can expand that if you need to for additional money.
7/C/b) The above suggestion kinda requires that you can create subfolders inside of folders. Also the color coded access right display is a good idea and it could be reworked to fit nicely with the 7/C/a version of right management.

8) Movement: Issues related to automatic movement.
8/A) When auto moving (say approach, or just plain auto move with WW or numlock) i often find myself in the need to avoid an obstacle and would press A or D to stray a little from my course. This on the other hand ends the auto movement. It should not really. The only thing that should end auto move is W or S for forward and backwards movement. All other movement actions should just be added on top of the automatic one, as if i would be the one pressing W whiele strafing.
8/B) When you auto move and then press W, the bot first stops completely, before it starts again. Suffice to say, the bot should not stop, when you tap the forward key in an auto-move scenario, only when you release that key.

9) Target locking: Issues related to target locking and pew-pew.
9/A) When you doulbe click a target in the landmark list, it starts locking and sets the target as primary, which is sort of okay. When you have a target locked and set as primary and you double click to target, it starts locking and sets target focus onto the new  target (that is not yet locked). This is horrible, as you stop shooting whatever you were shooting. It should work like this:
double click on an unlocked target, when you have no targets locked: lock and focus.
double click on an unlocked target, when you have a target locked, but no focus: lock and focus
double click on an unlcoked target, when you have a locked and focused target: lock but do not focus
double click on an already locked target: focus
9/B) The should be different displays for when someone is:
- in the process of locking you - say: yellow blinking rectangle
- already locked you - yellow rectangle
- is actually attacking you - red rectangle
- has you set as focus target (separate indicator from the above three) - some other visual added on top of the lock indicator rectangle..

10) Some issues related to reloading:
- You should not be able to reload a weapon, if it is already being reloaded. Right now it just restarts the reload.
- You should be notified about the lack of ammo BEFORE the weapon starts reloading
- You should be able to toggle the active / inactive state of a module while it is reloaded. Right now, if a gun is firing and is reloaded during that, you cant turn it off and if the target still lives, you will fire another volley before as soon as the weapon has reloaded.
- You should not be able to reload while the weapon is cycling.
- Changing ammo works dodgy at best.. when i had multiple charges in my cargo, i changed ammo type, then reloaded only to see the item default to a different charge. This was scanners or miners i think, but it might just be reproducible with weapons considering the reloading logic seems kinda similar.

11) Landmark list vs radar vs map vs main display: Again, the cheap answer would be - take a look at EVE for inspiration. But let's elaborate a little on that. when i go out to the field, i have 3 things i'm looking at:
- 1) the radar to gain positional information about my surroundings (disance / their relation to my position and to the terrain)
- 2) the landmark list to gain a quick overview of whats in my vicinity
- 3) the main view to do whatever i do.
As you can see, the 3 interface elements are used for drastically different things and as such would require quite different settings for optimal usage. For example:
On the radar, i do not want to see other players that i have good standings with, or even neutral / hostile players when im not in a pvp zone. Reason? I dont care what they do and where they are most of the time. What i need to know is where my targets and where my enemies are, so i would limit the radar to only show those, or show those with different colors: -> we have to be able to set the color of the radar blips based on various parameters and also we have to be able to specify what items we want to show up on the radar.
On the landmark list, i most probably would want to go with settings similar to that of the radar, but not neccessarily.
On the main view, i would want to see a lot more than on the radar.
11/A) Suggestion: Give us the ability to create specific display profiles where you can specicy all sorts of options,  including what to show in which color / icon. Then allow us to pick which one of our display profiles we want to use for radar, main view or landmark list separately.

The above list is by no means complete, but thats all i can remember from the top of my head. An interesting game you have here, hats off for that, but i'm also sure you realize that the bulk of the work is just beginning.