I had a problem with selecting ships and getting them to do stuff. I had to tell them to go to a sector, wait 1 turn, tell them to sell some stuff, wait 1 turn, buy, another turn, tell the ship to go somewhere else, and wait yet another turn. It was real easy to lose track of what a few ships were doing what let alone a dozen or more.

My fleet and other fleets had different UIs. With my main fleet, I could dock, buy, sell, shoot stuff, etc as many times as I wanted and still leave to a new sector all in one turn. The other fleets could only do one step at a time. It was like I was playing 2 different games at the same time.

I couldn't remotely transport VIPs or destroy asteroids. I had to dock at the station myself to pick up and drop off VIPs. I had to be present in a sector that was having asteroids so my ships could shoot them down. I found this inconvenient as I had to be multiple places at once, but could not. I literally got mission offers to destroy asteroids that were 1 day apart (travel apparently takes at least 2 days, even with fast travel tech).

I had some difficulty raising money. Rushing a level 10 steelworks didn't help. After being built, the other factions would take that opportunity sell me a lot of goods. I could not say no. I was poor for like a year or two as anytime I got money, it would be taken by the other factions in short order by trading with me. It made it difficult to buy goods for trade or to pay my station workers to do work. The station could do work without being filled to capacity, so I would have liked the ability to disable trade to other factions. Plus I had to pay transport fees...

There seems to be a point where the game gets unplayable. The list of ships get messy. The game started getting the list messed up (ships were not sorted in alphabetical order). I had a bunch of ships and thus I had to scroll through a bunch of ships in the drop down menu to select a ship I wanted.

Later, when I decided to 'finish the game', I started declaring war on different factions with the intent on claiming just about everything. The mess got a lot worse when I was using harpoons to capture ships. I got so many fleets in different sectors that it blocked my ability to select some sectors. I couldn't select them because the fleet icons were in the way.

It was also hard for ships to join fleets. Apparently, they had to be in the same sector to join a fleet. You had to select them once to move them, wait, then select them a second time.

You can't specify which ships you want to repair. I had a few fleets get damaged, but they were in sectors where I captured a lot trading ships. I couldn't repair my combat ships in one war as I was forced to repair everyone there.

I didn't like how I could only order maybe one or two ships at a time from the shipyard. Yeah, other factions deserve their turn to get their ships built, but I made a point to have several shipyards. I could deny access to other factions. I felt like I couldn't fill every slot. Also, the game didn't always show what was slowing down production (like a lack of fuel or steel).

Well, I had a lot on my mind. I might have more later.

- I would have liked the ability to disable trade to other factions.

You can. There's a check mark above each product that says whether that item will be traded. You can access this on the station details, or the Company Property screen, or on the System info screen.

- I got so many fleets in different sectors that it blocked my ability to select some sectors.

There are buttons on the orbital map to show other details instead of the fleet icons.

-It was also hard for ships to join fleets. Apparently, they had to be in the same sector to join a fleet. You had to select them once to move them, wait, then select them a second time.

You can merge fleets if they are in the same sector.
You can merge low number fleets into high number fleets but not with your main fleet.

On the fleet screen select the top fleet and edit it. Select each fleet below it and if the merge button is available use it. Edit the next fleet and so on. That should group all ships into one fleet per system. Then you can move them a fleet at a time and merge them again instead of a ship at a time.

- I didn't like how I could only order maybe one or two ships at a time from the shipyard.

Shipyards have different construction slots. I was able order 1 light and 1 heavy at the same time. With my own shipyards I think I might need to wait a day to add another ship to the queue.