In regards to having multiple fortresses. I would like to be able to take a break from a fortress and come back to it, but I accept the problems in doing so.
What I WOULD like, is a "surrender control" option in addition to abandon fortress. The player would never be able to take control of the fortress, but it would become a permanent fixture in the world like all the pregen cities.
Sometimes I create an amazing fortress that days of my time into, but it reaches a point where its pretty much "done." Sure I could do more with it, and come up with more challenges... But once I've created giant spires, with cavernous burial halls, and complex water system with magma falls and a legendary army, well, I'm willing to let the fortress go. But to simply leave it, like I would leave one of my horrible fortresses gone wrong, is just sad.
There should definitely be a difference between an abandoned, failed, fortress, and a successful fortress that the player is done playing with. Of course you would need to meet some sort of requirement before retiring it. Maybe a certain wealth and population.
I like all of the ideas. I especially like having information about the stones and minerals. It annoys me when I come across a new stone that I haven't seen in a long time and I have to check the wiki to see if its important. And then of course the fact that my lack of knowledge renders many of the stones from basalt to gray, and Cobaltite to blue. All blue stones become the same to me.
In regards to the saving. I have save scumed. I even savescumed a bit back with nethack. I understand why people would want a save feature. However, at the same time, a built in save feature would change the feeling of the game. (I mean a save feature where you could go back to old saves). When a game has a quick save, you play it differently than if you just have to go into a menu and save. If you have multiple quick saves its even different. It just changes a sort of mentality of the ramifications of your actions. Sure you can save scum. But when you do, you know its not part of the system. You know that you are killing a world that exists, and replacing it with an old one.
I also want to point out that this method of dealing with saves, is not just relegated to rougelike games. Sims 2 doesn't let you have save slots. I don't think Sim City 4 would let you. Its a trend among many simulations. In a shooter, you pretty much have only one goal, get to the end. If you end up stuck somewhere without any health and a bunch of enemies to kill, you don't have much choice but to go back to an earlier point. In a simulation though, the bad things can be just as important as the good. In XCom (which admittedly did have save slots) failing to take down an alien ship and letting them land and make a base, while not a GOOD thing, did open up a new mission opportunity that, while high risk, could gain you a lot.
That said, it sucks to loose progress to a bug or because, some part of the game did not behave how you thought it should. And as I said, I do save scum.