Regarding the command queue system, currently AI War allows you to queue commands together for ships to execute one after another by holding shift when making the command, so you can queue movements or attacks (but not mixed together in the same queue, and not changing ship modes in different legs of the journey). At some point, we'll hopefully getting a universal command queue system in there so you can do movements, attacks, wormhole commands, and mode changes all together in one thing, and that alone is very good reason to keep the current modifier system for setting modes when making commands, which is why I brought it up. Off the top of my head, I can't think of any other good reasons for why the mode keys shouldn't be toggles instead of command modifiers, though perhaps it'd feel less natural (at the very least, I think it'd be a pretty bothersome change for existing users. Trying to keep interface things fairly constant after introducing them is definitely a good idea
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As for the wormhole stuff, I had interpreted your comment about it to mean that if you accidentally ctrl+left clicked on the wormhole while you had units selected instead of ordering them through the wormhole with ctrl+right click, you'd no longer have the units selected when returning to the planet to correct your mistake (which isn't the case, save for an irritating bug in the current release). The issue of the ships not being selected on the other side of the wormhole isn't going to be addressed, simply because of existing limitations in the game's engine. I wish I could give you a different response for that, but it's unlikely to ever change.
Regarding the unit palette, I'm pretty sure it's ordered like when you press F1, so it should have a specific order that ships pop into. Does that help? I use the unit palette a lot to figure out how many of various ships are on the planet and to quickly select all of a certain kind of ship. On enemy worlds, it's also great for locating specific enemy targets (such as sniper turrets). Perhaps the order should be non-fixed, but I feel like that could cause problems of its own. Should be worth thinking about, though.
I'm glad you've been enjoying the game despite the complex interface! I'm confident you'll have a lot less trouble the more you play, and hopefully we can also get some changes in there to counter some of your complaints.
Edit: Also, I don't know if you know about it, so I figure it might be worth mentioning TBS-friendly pause, as it might be useful for you. You can enable it in the settings menu, as well as disable the screen dimming there. It lets you queue up all the commands you want while the game is paused, which can help move the game along at a manageable pace. I hope that helps.