As much as I loved the game while I was playing it I cannot really disagree with the points you made. It really is kind of a mess and man did it get repetetive after a while but when everything was still new it was so much fun just going out there and exploring the world, finding out new stuff etc.
I didn't even know you could get buildings as loot. The way the base building metagame worked was that you could go to a screen where you could see the whole map and look at your settlements. These settlments would consist of squares which you could building buildings on. All NPCs that lived in the settlments had a number of action points per turn and you could order them to either go explore a cave and bring back other NPCs or make them build stuff or just chop up wood and what not. The weird thing is that you could move around freely during your turn but for anything to happen you needed to end a turn and begin another one.
So again - it was messy and it probably wasn't such a great idea that they changed around the concept so much during the beta (afaik they released new versions almost daily), it almost looked like as if they didn't really think it through. On the other hand they were really, really great when it came to fixing bugs and implementing new ideas (as I said: patches came almost daily) and they wanted to make a good game.