Ohh... I see what you mean. Hmm, a few points in response to your questions, then:
1. Generally speaking, decisions you make in combat ONLY have a metagame impact if you want them to. Examples:
- If there is a civilian freighter, and you decide to attack it to draw away an enemy, then you lose some favor with honorable races, as well as the race in question. But you gained a tactical advantage that you could have potentially done a different way. Your ships would not have auto-fired on that freighter, so it would not have been an accident.
- You resort to nukes in the orbit of a planet. You're poisoning the planet (might be good or bad), and the planet's race likes you less. Might be good or bad. It's also a really effective weapon. But there are certainly other weapons, and you can use nukes safely away from planets without angering anybody.
- You try one of the new "defense" type missions and fail to defend what it was you were supposed to defend, but you yourself live. This really angers the race, and other bad things happen. So this actually goes against the "skill in combat doesn't affect the metagame aside from the game ending" note. The thing is, though, that there is nothing compelling you to have to take these missions in the first place; there is plenty of other stuff you could do. There's a risk/reward with these particular ones, and the risk might not be worth it.
2. Having your flagship blown up is something that can happen fairly easily on a moderate difficulty level, actually, but there is usually a lot of warning time. In other words, you ought to see it coming. If you go "I got this, I can pull this out!" too much, which is tempting to do, then yeah you'll die. Instead going into retreat mode, throwing some of your smaller ships under the bus most likely, and booking it out of there is good. But you have to recognize that this is happening before it does have.
3. Combat skill isn't something that is irrelevant to the metagame, by any stretch. Combat is a means to an end, usually, and if you can win certain really tough battles, then you can gain a metagame advantage of some sort. Here again, though, you can opt not to do these if your forces simply are not up to snuff.
4. There are some unavoidable combats, mainly from the AFA and assassins. But they are rare, and not that strong overall. They only come after 2 hours' gametime on normal difficulty, and only when you have really pissed someone off and are usually in hostile space. There are ways to avoid both of those conditions. The biggest threat of these types of combat are if you've just had a big battle and are still not at full fleet capacity (you just fly to any planet and poof you have full fleet capacity again), and then they catch you half-dead already. You can't retreat from this kind of combat, which can make them very nail-biting.
5. In terms of a "typical playthrough," I imagine that players will sometimes try something out, realize that the situation is worse than they feared, and then run away. With more experience, they'll do that less. How many times they do that is likely related to how adventurous they are in the first place, heh.
