On crafting spells -- it depends on what you mean. Not in the magicka sense, spells won't be craftable. You can't make up a whole new spell out of nothing. In terms of if you can affect existing spells via modifiers of some sort... possibly that might be something we add, but it's not in our immediate plans. You'll have to craft, well, pretty much every piece of equipment you find, though. That means you'd find an unpolished fire gem or something along those lines, and then depending on how you craft it, you can turn that into one of a small number of finished fire-related spells that you can actually equip. That's what the enchanter class is for.
On the civilization level -- no, this isn't a hint at any 4X or city-building components. The goal here is spending less than 1% of your time in a menu, same as with a Zelda game. I would estimate that close to 50%, if not far more, of a 4X game is spent in menus, and a good portion of a city builder depending on what you consider to be a menu (does the underground view in SimCity count, etc). Given that the game is post-apocalyptic, there won't be any new construction of buildings or similar, but a settlement will consist of people setting up homes inside existing buildings. So that office is my smithy, that cubicle is your "house," etc, that sort of thing. There may be smaller wooden structures that players or NPCs might construct, but we're not entirely sure on that yet.
Bear in mind most of the "city building" parts happen in an automated fashion, without any interaction from players. At core, that's what we're going for, as we want it to be more about the higher-level decisions rather than about the intensive management. So you invite X NPC to go to Y settlement, because they are an armorsmith and you need one there, etc. You set up the wind shelters as sort of a "road" of sorts, to allow for strategic movement on the world map. And so on, that sort of thing. The core experience, here, really shouldn't be any more complex than Zelda, Crystalis, or similar.
That said, there's a lot of room for optional things to be layered on, and given that we have civilization levels a lot of that can be gated for the protection of new players, too. If someone is interested enough to play past a few civ levels, the game is free to become gradually more complex, certainly, and that's the general approach Keith and I have been coming at it from. Right now we're mostly focused on making that core experience really tight and fun, so that if the game never grows beyond that, it's no loss for the bulk of our potential audience (and hey, that helps with scope, and with the review-ability of the game, and the ability to describe the game in a nutshell, and the ease of introducing new players to the game, and many other handy things).
Keith and I have talked about everything from having some much deeper advanced city-building components, to much more freeform advanced crafting, to having settlement-defense segments at advanced levels, to all sorts of things. Depending on how the public alpha, beta, and beyond goes: we might develop on that sort of thing as themed, paid expansions focusing on some new style of optional gameplay that provides benefits to the main gameplay and layers onto it; or we might just build that same sort of thing into the base game for free if the game is selling that well already; or we might just not get to it at all if the game's fanbase doesn't look like it would support it.
All of those sorts of hypothetical features would layer into existing worlds, unlike, say, Defender Mode in AI War, so that's one thing that is nice about it. This is "an adventure game about exploration," at core, and that's where Keith and I are mostly focused at the moment, but we've been keeping things open and certainly talking about increasing the scope of that, if the game is popular, and once all the rest of our requirements for the core part is met. And as new ideas occur or are suggested to us, of course.