Thanks for the detailed reply. I don't have much experience testing games -- a bit, but not much -- but I've worked as a writer / designer fairly extensively in the game industry, so I'm trying to give the kind of advice we found helpful on the other side.
1) It doesn't matter whether they get the range *right* (or optimal) -- it only matters that they set some value for the "close enough" range (first firing range? every gun can fire range?) and then have you stop when you hit that range. Presumably, "close enough" should be "every gun can fire," since if you want to stop sooner you can do so manually.
The "close enough" range would *only* be triggered when you had selected an enemy target and were approaching it, and would only be triggered by your proximity to *that enemy.* A fighter flying between you and your target would never stop you, and nothing would cause you to stop while retreating.
This is by far the simplest fix and I can't see any disadvantages at all to it. There might be better (more effective for battle purposes) places to stop you, but figuring them out is much more complicated. This fix adheres to the KISS philosophy and solves the problem.
2) Racial similarities. The problem isn't the way they fight (or look), but rather the way they function diplomatically. They seem decently delineated from a combat standpoint, but combat isn't the be-all-end-all of the game, and I see no reason not to distinguish them more. Moreover, the Cloak of Babulon seems overpowered as is.
4) The "do over" is better than nothing, but seems nonideal by both favoring experience over strategic thinking and not granting player flexibility. If I'm already suped up, some trinket isn't necessarily what's best for me. A teleportation might be more valuable (especially if I don't have hyperdrive and want to save a "get home immediately" charm); so might wiping out a foe (he's an assassin, right?).
7) Well, chalk this one up to the rules on loadout not being clear enough. I just thought he couldn't change gear (not that it was some fighter rule). Is there any reason not to give the player a message like, "Fighters can only equip [this type of component] in [this slot]" when you try to put the wrong kind in?
8) It takes one day, right? Seems too low-cost, especially given how relatively easy it is to get one of those helmsmen. Hyperdrive takes 60 days, and feels rarer, doesn't fight for you, doesn't expand your cargo capacity, and doesn't get you friendly with the Zorg.
9) I think you're confusing two kinds of knowledge here. Imagine if Solitaire (Klondike) were played more or less as it currently is, only black eights go on black nines (and red eights on red nines), queens can stack on kings *or* fours, and the Jack of Clubs and Three of Diamonds are wild cards. Now imagine that this game boots up just like normal Solitaire. Whatever the merits of those rule changes, the benefits are completely swamped if the rules aren't told to the player, because it's simply unfair to expect him to learn by trial and error such trivia.
Now, if those rules *were* told to the player, obviously they would take a while to get a handle on, since it would introduce extraordinary complexity to the game (or, at least a little more complexity, especially if you were playing, say, Freecell rather than Klondike). You'd need to learn new strategies and whatnot. But you'd be learning those strategies in the context of completely transparent rules.
Right now, the problem is that I just have *no idea* what it means when I read weapon descriptions -- I don't know how much punch they pack, I don't know rate of fire, etc. And if I didn't read the manual, I'd never know about point defense (or was that in the tutorial?).
You describe drives as a "counterexample" to the general rule, but drives fit with the general rule and weapons are the clear exception. Shields give a plain hierarchical description (afford little protection, some protection, etc.). The computers give a plain description. So do drives and thrusters. (Moreover, money makes ranking them easy.) Scanners are clearly ranked. Repair modules are ranked. ECMs are ranked. But not weapons. It just seems silly to me.
If nothing else, it would help to have clear ranks within each class of weapons, and a quick mention in the tutorial what each class of weapons is appropriate for *generally speaking*. "Missiles are the best way to take down capital ships, while beam weapons tear through fighters." If there are special wrinkles, let the player discover them, but give him the basic rules.
11) Does money transfer between stores? It didn't seem like it to me. Do you only get scored for your coins at Glory?
13) That's really helpful re: coins. I had thought value was randomly determined each game and then there was some modifier based on class that only came in at score. It's a little weird that the galactic market price is determined by the preferences of one customer, but that's fine, I guess.

I'm inclined to think that it would work better with fixed prices and then multipliers / modifiers for the score, but it really doesn't matter much.