I just finished the game for the first time last night and I'm knee deep in my second playthrough, and a I strongly disagree. Armstrong is perfect for this game. What tone are you talking about? The entire tone of the game felt like Doctor Strangelove to me. It's an indictment of U.S. foreign policy for the last 13 years. The funny thing is this game's story had more to say in six hours than the entirety of MGS4. The beauty of Armstrong is that it's a reflection of our current political state. Maybe I'm just projecting, but Armstrong seemed like like a combination of George W. Bush (University of Texas), the Tea Party and Any Rand-ians and fighting him was god-damn awesome. The fact that people think Armstrong's awesome or that they are saying, man, well, I can can kind of agree with him blows my mind. When Raiden said he was "batshit insane" I was fist pumping into the air. We're so used to the Metal Gear franchise being so super serious, but, seriously, the Armstrong fight was some Mark Twain level of satire.
If this is just a side story, I can't wait for Ground Zeroes because Kojima said he'd be tackling "taboo" subjects. The fact they had the balls to even set a level in Pakistan with this game earns my respect.