Hey, things are getting interesting now. So I'll take a break from the deep future of my own universe, and the intergalactic invasion that is underway there, for some Star Control!!! I've only read the text file so far.
I think you are exactly on target focusing on the planet, that is the by far obvious place that can be transformed in a modern way that everyone will agree is an improvement.
The mushrooms on Venus are weird, I understand the comment someone else made about them... by I LOVE the look. I don't know the story of why Venus looks this way, but I really like this screen a lot. Everything about it really. The planet... the color. Before color I always used Amber monitors instead of green... I love the Amber, it is almost nostaligic too me as the computers I used right up until Star Control came out. And the mushrooms genuinely have me woundering how Venus came to be like this, so it works on that level with me as well. I just really do like the look, though.
On the supermelee screen I can see that your solar systems are actually very small. A lot smaller than I had been thinking. This is a good thing. The smaller the better until it is too small-) From this screen it appears that you may be at a very good size for the whole map, but hard to tell from just this map. A lot smaller than what I was thinking, though. You really don't want to fight a Klingon or Andromedan on an open map.
Modular ship design... got it. Romulan Hawk Series, I've done that one before... Is it permanent or can you change the modules at any base that has them like my Romulan's can? 
I like that you are keeping the mothership weak in the early game and forcing the use of satellite ships. There are other ways of forcing the use of satellite ships in the later game as well. Through story “The weapons on the big ship are broken right now, sorry, use the little ones”, terrain “the big ship can't go there, but the little ones can”, and opponent “that thing will probably kill the big ship, but the Chmmr kills it easily”. And other ways I'm sure you will see when you get there. In my mind, if the player always uses the big ship, and never uses the little ones, I completely failed in the design of the game. If I was making it, and critiquing myself.
That thing about customizing the shape of your ship will never go away. Sleek and thin is always going have an “inherent evasion advantage” over big and bulky, and nothing can change that other than cheating with hitboxes or something like that. The size and shape of the ship ARE a part of it's balance, a big part! I wouldn't fight physics, I've never seen anyone win that fight yet. You can, of course, cheat. I would if I could make it work, and I wanted that thing. “Illusion” is my style. So if you can do it in a technical way, say with the hit boxes, that the player won't notice... AWESOME!!! SVC might have even give you a Battle Star for that one if you did it in his game:-)
The easiest “AI” for wingmen is to lock them in place in a V or Diamond formation as if the formation were a single ship. They mirror you PREFECTLY as if a single ship. The fire with you... “concentration of firepower at the option point”. I didn't say it was the most realistic way, just the easiest way... and a good starting point to expand into something more realistic from.
I assume by the comment about tilting the camera angle a little in combat you meant the default setting and I can still set mine into straight top down and leave it there. I don't need to play it, I have enough experience with these games already to tell you that I won't even want to play it if I can't play it that way. There are a lot of others that won't as well. It really is a huge deal that messes with a whole lot of things. Of course, as long as I can set my screen that way... I don't care if others want to disadvantage themselves against my perfectly clear vision of all aspects of what is going on:-)
This all looks really great too me. It really does. I actually can't wait to play the full adventure game now after seeing all of this, and up until now I had just been dying to get my hands on any computer top down space shooter again because it's been since Subspace that on existed. Now I am really wanting to play the full game a lot more than just having Supermelee as my version of a FPS game, which is what they are too me. They are my FPS games, and FPS take a distant back seat too them:-)
I haven't looked at the movie file yet, I'll have to look at that later.