Edit: Argh, tried to respond to everything in-line, but I can't make the forum software do what I want it to. Some quotes are block quotes, others are direct quotes. Sorry, everyone.
To your first complaint, mousing over the research button will show you both what is currently being researched and it's progress and what's queued up behind it.
As for knowing if you need more research stations, again, mousing over the desired research will give you the information you need. The background of the tech trees also changes colour as you gain more research stations to show what you can and cannot research. I'm fairly sure stuff you've already researched "pops" out more and has a border around it, and as you progress, you should probably know what you have researched anyway.
Ah! Interesting that I didn't notice that. I'll have to go back into the game and make sure that is working for me. Regardless, I would love to see that become part of the actual HUD, though, without a mouse-over. It wouldn't take much screen real-estate.
Also, if you have an object selected, all you have to do to bring up the infocard is mouse over the big picture of it in the bottom centre of your screen.
Okay, so that's a bigger target for the mouse-over, but still requires a mouse-over. If I have already selected something, I would prefer to have the information immediately available without further navigation. There's no reason to add extra steps between the player and relevant information!
As for seeing emblem instead of ship type... I don't think I've ever had that problem, at least not noticably, I'm going to have to go and fiddle with game options to see if you've enabled something, I normally see a distinct icon for each ship type.
In response to primary interface issue 1) this may be a bug you've encountered. When zooming out to view the gravity well, as I assume is what you are talking about, each ship type should be colour coded to faction and have it's own specific icon. Same thing for structures. The only object inside the gravity well to have the faction symbol on it should be the planet. Correct me if I'm wrong though.
Hrm, yeah, all I see is my faction's emblem - not icons for the ship types. I wonder if this is indeed a bug, then?
When you zoom way out, all you can see over your ships is your emblem, overlaid all over itself. This is really unhelpful - you can convey the same information simply with color. Why not give us icons to show us ship type, in the color of the player? Seeing a huge cloud of my emblem totally doesn't help me organize anything.
Your solution can be a problem in multiplayer when the color show is not the player color but the team color... it will become impossible to know if it is one of your ship or a ship from a team mate... it is why the emblem of your faction is useful...
I understand your concern, but I think there must be a way to achieve both. Maybe have two rings, one with team color, one with faction color; or maybe include the faction emblem, but just make it a very small icon off-set from the ship-type icon.
Either way, right now all I see is a cloud of faction emblems, which doesn't tell me anything other than that I've got a bunch of something in that general vicinity - this is next to useless when your empire has grown.