ChouToshio's post has been one of the few posts in this thread that have actually made a solid argument for Salamence being OU. Residual damage does hurt Salamence greatly, usually allowing it to switch in only 2-3 times. However, I think there's a hole in that argument that wasn't sufficiently addressed. Salamence isn't Flygon. It doesn't need many switch-ins to do its job. So although switching it in is a risky move, it at once seizes control of the board (continuing your chess analogy here). Now, I'm not a pro at Pokemon by any means, but I did make it to over 1400 on the ladder pre-Latias ban, so I think I'm at least decent at the game. The assumption that a lot of people are making is that the player using Salamence will just switch it in on any resisted attack and attempt to set up or grab a quick kill. This is anything but the truth. I rarely, if at all, see good players bringing Salamence in on Turn 4. Salamence's go-to switch-ins and revenge killers are easily lured out by other threats. Like you said, Scarfed Flygon isn't going to be hidden in the last slot, because it's built to scout and revenge kill throughout the game. Salamence isn't going to be brought out while that's around (unless you anticipate it switching in and fire off a Draco Meteor). When Salamence does come out, it has precisely the effect of a Queen in chess. Suddenly, it becomes the center of attention. Nothing else in OU has that kind of presence. I don't think it's exactly balanced to have a Pokemon like that in the metagame.
I would also like to add that the game doesn't end when you kill Salamence. A lot of posters have repeated again and again that even if you switch in a bulky Pokemon predicting MixMence and let it get off a DD, that you can revenge kill it by forcing it to Outrage. Ice Shard users, Scizor, Scarfed Flygon something else bulky enough to take a +1 Outrage and 1hko with Stone Edge or Ice Beam. I'd like to point out that every almost single one of these commonly used revenge killers gives another Pokemon a free turn. So you switched in Weavile and got rid of Salamence with Ice Shard. Good for you. Now Gyarados has a free turn to DD, or Metagross has a free turn to Agility, or you also lost you revenge killer in addition to what you lost to Salamence. How many Pokemon carry a Choice Scarf just to revenge Salamence? How many of those Pokemon are going to be locked into a resisted move after they revenge it?