2) The sidebar list. I don't care how many extractors or research stations I have on a planet. I need to find my factories fast so I can change way points and issue construction orders on the fly.
Since way points are set on a system level basis, just select the planet to do that. And since factories get controlled from the planet screen too, same there.
3) I need the buy/sell metal and crystal buttons on my main screen. I buy/sell a lot and all good players will.
Personally, I've been pressing to get them to have a left click buy, a right click sell, a given resource.
4) I'm not sure how many capital ships are supposed to be in a normal game but how about a zoom and select nearest capital and have that button rotate through them all.
... Why?
4.1) When something is being researched, replace the research icon with a progress bar + name of what is being researched.
And when the devs finally break down and allow concurrent military and civilian research?

6) Colony ships. Can we get rid of these please? It's useless micromanaging and since there is no penalty for having a bajillion planets, there is no reason not to colonize everything. Make it so the pop goes to 0 and then if I have a majority military presence in the area, the planet shifts to my control after a set amount of time.
Um, no thanks. Thats a rather drastic mechanic change, and the removal of colony ships means you no longer need to cart (escort) a fragile vessel around with you early game, or pay big bucks for the Akkan late game.
7) Tech tree. Stuff takes a lot of research centers. The amount of centers needed for technology should be scaled based on the size of the map. I find in 1v1 and 2v2 maps I can never get very far into the tech tree.
And on larger maps you can hit the cap too easily. That, in a way, is the point. Many of the higher level techs are unbalanced on smaller maps (cap ship research, insurgency, planetary bombing improvements, the construction boosts and the economy stealer at the top of the civic tree, tec etc).
In order words I would like MOAR UNITZ!
Why? You have plenty. Sure, in early game you don't use them much, but in later game LRM frigates and siege frigates become vital, and carriers are
powerful units to control a star with (as well as taking out defenses) and therefore make the flaks needed. Hoshikos / Cielos are also quite powerful, and the Kodiak verges on replacing the Cobalt.
Siege ships. These ships are dumb, charging stright into a planet to kill it. These ships also have only one purpose which kinda makes it lame. These ships should be able to damage other ships, maybe give them splash damage as well, like land based artillery. Current system is, clear a path, them pahse in siege and guard them. Hardly interesting or fun.
First off, siege ships do have the power to attack ships. They just suck at it.
Also, having them be a purely anti-planetary force makes sense gameplay wise -- they're a specialized unit, powerful at their role, but vulnerable to just about anything else. You have to protect them, and their presence in the game means that there is a clear difference between a
raiding force and conquering force, beyond size (aka a fleet optimized for raiding can't really conquer, however large it gets).
10) Formations? I dunno, ships just overlap each other and if not zoomed in, 3 ships could actually be a cluster of 7 ships.
Ships do tend to move into formations, though they don't maintain them. And yes, ships do fly above/below them, personally I like that -- gives them a little bit of horizontal concentration.
11) Counters. Most good strategy games have counter units. As it stands now, having more units + more tech will win me the battle guaranteed. And by more units I mean more quality units, of course 3 cobalts will die to 2 capitals. If a 10 Cobalt + the starter Capital comes at you, what is your counter?
If a carrier heavy force comes at me, I counter with flaks. If a LRM heavy force comes at me, I counter with carriers or jump-positioned Kodiaks / cobalts. If a kodiak heavy force comes at me, I keep my carriers at a distance and pound with fighters, or LRM ships.
If a 10 cobalt + capitol ship force comes at my home world, I fall back on the repair center and let my Sova's fighters pound the force until it either comes to meet me, or is clearly bypassing my defenses, at which point I take it in the rear.