Some agreement, some suggestions, some mentions of things which I'm pretty sure have already been mentioned before.
Free pan camera during battle
Potentially nice to have, but could mess up all kinds of assumptions regarding fog of war, view distance, enemy ships, etc. As it is, you can change which friendly ship your camera is focused on from the tactical screen - not sure what extra useful functionality a free pan camera would offer?
Ability to see opposing fleet while choosing ships for deployment
Would be nice, since you can see it before combat but not after you start combat and go to the deployment screen.
Ability to pin/highlight/label points of interest on the map
Would love this. Has been requested multiple times I believe, to add notes to points of interest (note which systems have areas/items of interest which aren't readily viewable from the galaxy map or system info screen, notes attached to markets/planets, etc)
A way to quickly move dozens of weapons between cargo and storage/market
Ctrl-click moves an entire stack (buy/sell/transfer), shift-click will let you rapidly select a specific quantity of the item to pick up. Ctrl-click will also transfer only enough of a stack to fill up your available capacity (or to bring you down from being over-capacity to the max) the first time you click.
A way to mark for sale weapons in excess of X owned
Could be useful, but generally at the point where you own so much of a weapon that you need to sell off the excess, the amount of money you make by selling the excess is barely worth it. At best this would just cut down on hoarding 500+ of common/small weapons by endgame and earn a few extra credits a month on top of the hundreds of thousands you'd already be making.
A way to consolidate weapons easily into one location
Could be interesting to have personal AI convoys be generated to move your personal goods between your colonies if you're moving your main base of operations. However colonies also already transfer anything they generate automatically to a designated primary colony, so the only way this would happen is if you manually stashed weapons at a bunch of different colonies.
A way to auto-sort your fleet
Never really thought about this, since fleet order these days is purely aesthetic. I generally already manually order mine by size and D-mods and combat vs civilian duty. Might be nice to have an auto-sort which does that, but then of course everyone has different preferences since there's no real gameplay reason for ordering your fleet.
Recovered ships returning to the same spot in the fleet instead of the bottom, reassigning officers automatically
Would definitely be nice.
When your flagship dies, move your character to an unoccupied ship instead of ejecting an officer
What if you have a small fleet your next unoccupied ship is a civilian ship and you forget and end up flying into battle in a Prometheus? I think it's better to just move to the new first ship in your fleet order, whether it ejects an officer or not. Or remove you entirely from the fleet and warn you to pick a ship to command at the start of the next combat if you haven't already.
Ability to repair at a dock from the refit screen
Repair individual ships you mean? There's already a "repair all ships" button when you first dock at a colony, and it will ignore ships in your fleet which you have turned off repairs for in the fleet screen.
Ability to reorder ships from the refit screen
Could be nice, but why not use the fleet screen? Maybe instead, the screens could be further combined so that the refit screen is just a part of the fleet screen or a popup screen when you choose to refit a ship...
Access to the codex from the refit screen
I think Codex accessibility and content is one which has been brought up before, although the weapon and ship info cards are already readily available in Refit by mousing over a given weapon or the "?" next to the ship's OP bar respectively.
Access to the ship purchase screen from both the refit and market screens
The "F" shortcut for the Fleet screen (which doubles as the ship buy/sell screen at colonies) is useful. It should also have a button on the bottom bar at almost all times.
A way to "test drive" and "test outfit" ships before purchase
Maybe nice, for new players. But test-driving items before you buy them isn't very common in many games in the first place because it can lead to eliminating any risk and most sense of discovery. The Codex and ship info cards already have all the pertinent information, and the one-shot missions from the game title screen can be used to test-drive ships if you want to just have fun outside the campaign with ships you haven't purchased or manufactured yourself.
Ability to click and drag to rearrange the order of fighter wings in bays
The same reason you can't click and drag weapons between weapon mounts, most likely. Though in this case all fighter bays are the same in all ways, so it could make sense to treat them like a list rather than unique slots. Probably done the current way for Alex's convenience.
When fitting weapons, ability to sort weapons by type rather than listing
Would be nice if the sorting method was customizable. Personally I like it being sorted by source -> size -> OP, since at the stage of game when I don't readily have access to all sizes of weapons already I'm usually also on a shoestring budget and can't afford to buy a bunch of Large weapons to fully outfit a capital ship.
On missions screen, ability to remove/hide exploration points of interest from your feed
Definitely already been mentioned, and I know Alex is adding a "remove" button for intel which doesn't already automatically expire.
Ability to tag missions so that a clickable pop-up describing it is visible on the overworld screen
Could be useful, could maybe be tied to the "Important" list (since you can already mark intel items as important).
Ability to see crew level and skeleton crew required on overworld screen
Not really sure what benefits would be gained vs the extra real-estate. Crew level doesn't dynamically change while you're flying around, unlike fuel or supplies. Maybe a bar for supply level to go with the fuel level one could replace the existing numerical supply ticker.
In combat, when selecting targets with R, the first check should be for ships
This would be nice if it's an issue, though I can't say I've had an issue where there are so many fighters overlaid on a ship that this has been an issue. Generally fighters seem to try not to hover on top of ships. Only issue I've had with targeting is selecting ships in the tactical overlay which are all right next to each other.