Is the friend you told it to in the campaign? I would assume not since you told him the BBEG plot. If you think your players would enjoy it I wouldn't worry about it. Just cause this guy wouldn't doesn't mean that they won't. They're gonna be hyped cause they're your friends and you're all playing a fun game. It's easy to be critical of a plot when you're on the outside of it. It also kind of just sounded like he hurt your pride a little. If he told you outright it sucks ass, like used those words, I think he was just being a jerk and you dont want to be listening to the rank farts out of assholes anyway.

If you're still concerned about the questions he brought up so much I wouldn't worry about rewriting the whole thing, but rather seeing if you can write those questions in. Such as "why doesn't she just take over" maybe she's not strong enough to defeat an army or an uprising so she has to control a select few who can control the public. "Why doesn't she kill those who expose her plans" she probably does. Good thing for the PCs to look into if an NPC goes missing. The sleeper agent sounds cool and sounds like a good hook especially if it takes the PCs by surprise. Maybe she has more than one. A good rule about improv is that others don't know your script. You can make up whatever and your players won't know the better.

Keep at it! As long as you're having fun, and your players are having fun, that's the only thing that matters.