I absolutely love
http://www.cartographersguild.com - such a great resource and a great group of talented people - if you check out our devlog you'll notice we used an algorithmic, procedural style that I learned about through The Cartographer's Guild though in the end we rejected it in favor of the more hand-crafted and fantasy themed (and easy to make) Campaign Cartographer maps.
These are all fantastic questions, most of them were answered only after significant internal dialogue in our team. Let's hit them point by point.
1) Initial release has 15 custom agents, with the number you can recruit at any time dependent on which Old One you've chosen and how awakened your Old One currently is. To answer the second part I need to explain slightly how Agents work, Agents are "available" once they've been corrupted, so if you can satisfy the requirements for an agent they are considered available to you even though they haven't yet been recruited onto the map. When they are like this they offer passive bonuses, for instance if you satisfy the requirements for Baron Greywind he passively lowers Order throughout his hated cultures region, and any battles there will be assisted by some of his legions. If you recruit him as an Active Agent onto the map, you lose that bonus. You can corrupt Heroes and they operate similarly, giving you a spy in an adventuring group, army, or state depending on the location of the hero - when you "activate" them they join your side with their current stats intact and any "corruptible" abilities become their corrupted counterpart. If they were in a precarious situation when they were activated, such as during combat, they will often do something deterimental to the other heroes before vanishing. Heroes stop leveling after they join your side, and operate like all other agents.
2) All of the guilds have special actions that can be taken, turning the thieves guild into an assassin's guild is unique to the "Underworld" guilds, but some of the others have corollaries. For instance, the Mage's Guild can be told to focus on a particular type of magic and the Merchant's Guild can begin selling mercenaries.
3) Currently that's not possible, the Chosen One would eventually declare himself and sages would SLOWLY figure out you were awakening and they'd raid your lair. It would be pretty easy to mod the game and allow it however. We WERE thinking of doing a scenario that you stay in deep slumber UNTIL an adventurer stumbles over you and awakens you, but it may not work out to be fun.
4) I like how you phrased this question, there is a "cultural limit" that most nations will go to when it comes to warring with eachother. In general they will fight limited wars for strategic objectives (which may be not so logically strategic depending on their personality) - in order to get them to commit their forces and fight a total war or a war of annihilation they'd have to really hate eachother, which CAN happen randomly but is unlikely without your intervention, either preventative (stop leader and bard type heroes from swaying public opinion and leader decisions) or purely malicious (staging border raids and massacres, inciting the peasants against a culture).
5) Yep, new civilizations are pretty easy to make. You need a culture to assign them, and a leader to rule them then you just specify their government type and you could drop them right in. Culture determines the "personality" of the POIs, mostly villagers, the Leader determines the political stance of the nation and its potential, and the Government Type effects its available actions when determining what course to take.
If you guys have any feedback on this stuff please let me know, I love hearing about our design choices and what you think sounds fun or what maybe we should explore doing a different way.