Actually, all of those games you listed except Darklands are turn based, they play in real time but they're divided into rounds.
Both sides carry out their tasks at the same time, though. Wouldn't call that taking turns. You could call it round-based, I suppose.
You may have noticed that in DF, it appears that combat takes place in realtime. Really, the game is turn based- every step is a turn. Actions are broken up based on how quickly a given character can make an action. So if a character with high agility fights an opponent with low agility, then on turn 1 char A attacks, and on turn 5 char A attacks again, then on turn 7 char B attacks, and so on. They are taking turns- its just that the turns are not equal in duration nor frequency.
As regards combat complexity, yeah, if you give an untrained guy a sword he's just going to flail wildly and it is mostly up to chance if he hits an arm or leg or nothing at all. If that same guy practices with his sword, however, he's going to learn how to use it and get better. You can even see this a bit in Minecraft- when you just start out, or get surprised, you pretty much just flail as fast as you can in the general direction of the enemy and try to get your bearings. When you've got a few combats under your belt and see the zombie coming, however, you can time your attacks to hit as soon as the enemy gets in reach, and you'll rarely take any damage in those fights.
What I'd like to see is some more depth to the combat- different enemies having different timing to their attacks would be an easy way to start. You could also have puzzle enemies who are only vulnerable at certain times or after certain actions (you have to shield bash to get them to let down their guard, for example.) You could have enemies with certain fighting styles, or a simple balance mechanic tied to blocking and attacking, or combo based combat, or any number of things that would be better than the "mash the attack button" thing Minecraft has going on. The real question is picking a system that will work as well in a multiplayer format as well as a single player format.