Have you even read the last adventure, or are you just imagining how you would write an adventure with the bard as a villain? Because the scenario you describe has little if anything to do with the state of Korvosa in adventure six. Spoilers follow, read at your own risk.
[sblock]
The city hates her. The city hated her when the king first married her for being a foreigner, kept hating her as the king's wife for her greed and fiscal irresponsibility, and their hate grows even stronger when she finally reveals what an insane, crazy, evil villain she is. Not even the decadent nobility likes her. Ileosa is not a student of Dale Carnegie's course, that's for sure.
As far as her government is concerned, one of her ministers tried to kill her, and only failed because of plot (I mean artifact!) immunity. The rest of the military seems more than willing to conspire and plot rebellion with the PCs. Even her 'fanatically loyal' Grey Maidens are brainwashed and tortured into their 'loyalty;' the module even states that their loyalty stems from [Ileosa's lesbian lover]'s small kindnesses to them than the actions of Ileosa. And the queen has even managed to lose the allegiance of the one person who probably should stick with her to the end, the aforementioned Captain of the Grey Maidens.
The final confrontation with Ileosa, of course, takes place outside of the walls of Korvosa, and in the final boss encounter, she doesn't even have any minions to bardsong. Wow, that's some great planning, Your Majesty.
As an NPC, it doesn't even really matter what her Diplomacy and Bluff are, since Paizo has created a great many NPCs with poor social skills and Charisma but lots of tough followers. She convinces the king's brother to poison the king...which is still kind of impressive. She doesn't commit genocide either; she creates an obvious plague scheme to kill those wretched poor people for no particular reason. As it turns out, the ethnicity she hates most has a resistance to the disease.
The PCs, as I have mentioned, have probably figured out that Ileosa murdered the king fifteen minutes after the deed is done. If not, they'll certainly figure it out (in the typical PC 'no evidence' way) the moment they see those plague doctors, especially if they were one of the million people who played Neverwinter Nights. And they acquire solid proof at the end of the second adventure. Ileosa's no Keyzer Soze, that's for sure.
You also state that Ileosa has some sweet allies...yeah, that's pretty true. I mean, for the adventures to mean anything, there has to be some tough monsters and villains to beat down. As a villain, however, Ileosa seems to succeed more from the demands of the plot than any personal competence or intelligence.
It seems to me that you're describing the adventure as you want it to be, not as it's actually written. Her schemes are pretty transparent, her control of the city tenuous at best (there seems to be a pretty good chance she'd get overthrown in a year or two without any actions from the PCs), her popularity starts off low and only plummets. She doesn't have control of the military or the priesthood (the high cleric of the predominant Korvosan faith is in the Resistance, btw), and the wizardry, while as evil as she is, don't want to get involved-and disinterest is not an attitude you want to cultivate in your subjects. Even the boss fight is something of a cakewalk, like the first easy stage of a boss battle in a videogame.
Again, this is from someone who likes Curse of the Crimson Throne. It has a lot of parts that annoy me as a DM, but it would be pretty fun to run or play through. But I like Rise of the Runelords more. [/sblock]
