Sounds to me like he has you pegged as firing at pots a lot when you didn't really hit. One idea would be to reign it in a little - stab at pots less when you don't connect with the flop. When you do connect, be willing to go all in over his re-raise and see if he'll follow you. He can't always have something, so take advantage of your opportunities. It also sounds like he has you pegged as a fairly timid player who will fold when he raises you, so you need to show another side. Stab at pots less, but raise more when you hit anything worth raising on. If he raises your top pair, re-raise. Be willing to go to the mat with a solid hand.

Another idea is to integrate the check-raise. I'd be tempted to use this both as a bluff and when I had a decent hand. To set it up right, you would first change your post-flop betting for a while; start checking the flop even when you raised pre-flop (I know - I've read Brunson too, but do it a few times anyway). Let him take a few pots without much struggle from you. Then pick a spot, either when you've hit big, or just when it seems like a good opportunity, and check-raise him with a nasty overbet. Let him chew on it. If you have a real hand you have insurance if he calls, but the real purpose is to unveil a new tactic and force him to back off on raising your flop bets. You can also try a minimum bet, which he'll probably raise, and then you can re-raise him... similar to the check-raise, but it comes off a little different and doesn't cost much more.

Finally, if you are really concerned about this guy (which is reasonable, since he seems to be both smart and aggressive), stop giving him options. In a short-handed game (once it's down to 4 or less players), if you hit a good hand before the flop - push all-in. Every time. Make him play coinflip poker. I usually save this for those hyperfast SnG's on PartyPoker, but it's a reasonable counter-tactic against a player if you suspect he's just outplaying you. You'll either see him fold more, or you'll put yourself in situations where you have a 50% chance to put him out of the tournament. If he's giving you as much trouble as it sounds like, a 50/50 shot to beat him (and double up, and therefore probably go on to win the whole thing) isn't so bad. I have only one player in my home games who really gives me grief; like your guy, he reads people remarkably well. I will gladly push all-in against him pre-flop with a decent hand, if we're in the later stages of a tourney. Because I know he's going to put me to that decision on the flop or turn, I'd rather force him into the decision himself.