If you REALLY want to have dragons that are fearsome and dangerous to everyone, you need to try out the Grim and Gritty rules, as seen here:
http://www.swordsedge.net/Grim-n-GrittyRevised.doc Basically, everyone gets 15 hp... EVERYONE... but armor grants DR and other things grant AC (now "Defense"). Since Soak practically replaces HP, things can get a lot of it, and so to overcome it, attacks are an opposed roll, and you add the difference between your attack roll and their defense roll to your damage. Criticals work by rolling a certain value over the opponent's defense, and criticalling gives you the chance to do things like break limbs, put out eyes, or just bypass some armor... other than these things, it's still d20 like everyone knows and loves.
It completely messes up the CR system, making some normally scary monsters chumps, and making some normally chump monsters REALLY SCARY. Dragons are one kind of monster that gets really scary. I ran the above encounter over again, using the GnG system... and Derrick the uninspiring still wins on average, but no longer gets out unscathed and has at least a 5% chance of dying INSTANTLY in the first round. Of course, if criticals are rolled, the dragon might also be able to tear Derrick apart in Melee as well, but the odds are still against the dragon.
GRIM AND GRITTY CR"13" versus ECL20
Young Adult Red Dragon
Soak: 31 (+5 con +18 nat +8 size)
Defense: 17 (+19 bab +0 dex -2 size)
Derrick the Uninspiring
Soak: 15 (+5 con +9 armor +5 nat -4 size)
Defense: 42 (+23 ref +6 dex +1 size +7 shield +5 deflection)
It doesn't matter much who wins initiative. The dragon is far away and plays it slightly smarter, giving itself Mage Armor, which is a deflection bonus and thus adds four to defense. It then flies in, a stereotypical strafing run. Derrick still save on anything except a 1, in which case he takes 4d10+24, average 46 minus Derrick's soak, which is only 15. Charred Derrick dies instantly, but that's only a 5% chance. Note that if Derrick hadn't had Improved Evasion (say the dragon wasn't fighting a rogue) then on a save, he would have taken 23 (-15 soak = 8) leaving him alive, but moderatly wounded and suffering in the future, meaning that the rogue in fact has a better chance than many epic characters of winning.
Derrick rushes in, granting the dragon an AoO. At a +27 attack versus a +42 defense, the dragon needs to roll a 20 or Derrick needs to roll a 1 in order for the dragon to hit (a little less than a 10% chance of a hit, in other words). However, on such a hit, the dragon deals 19 (-15 soak = 4) damage, not enough to really injure Derrick, but enough to make Derrick nervous.
Now Derrick attacks. With a +30 versus a +21, derrick will win by 9 on average, threatening a critical because it's a rapier. But since the Dragon's Soak is 31, Derrick's rapier won't be able to deal any damage at all (and thus no critical effect like blindness) unless Derrick bypasses the dragon's natural armor (finding a loose scale or whatever), which has a -8 confirmation penalty, making Derrick role a +22 vs the Dragon's +21, only a slight edge, but a reasonable chance. If Derrick wins, the dragon will take an average of 12 damage, putting it into the severely wounded catagory, giving it a -2 to all future rolls. If the dragon wins, again, the dragon takes NO damage at all.
The dragon now casts True Strike and bites. True Strike grants a +20 to attack (unless you house rule this like I did in my GnG game) making this attack a +45 (47-2) verses Derrick's defense of +42, meaning that it will usually hit by about 3 or so. This will deal 2d8+13, for an average of 22 (-15 soak = 7). Assuming Derrick has taken no damage so far, that STILL places Derrick into the Moderately Wounded catagory, making him take a -1 to all future rolls.
So Derrick now Sneak Attacks using Improved Feint and Skill Mastery to take 10. Assuming moderately and seriously wounded, respectively, we now have a +29 versus +19, causing Derrick to win by 10 on average again, again threatening the critical. This time, if the critical confirms, the dragon is dead even if he'd taken no damage aleady, but if not, we have 1d6+5+10 normal damage (average 18) plus sneak attack, which is a flat plus 20 under GnG... for a total of 38 on average, -31, that's 7 more life gone and if the dragon was wounded before, it's dead now.
Assuming that the Dragon survives this, there's still a chance it can do a bit more damage to the rogue, but the rogue can deal damage faster, as long as the dragon stays up close. The dragon could always run away, trusting in soak to not be SA'd, and then giving the ol' 5% instant kill breath weapon another shot in 1d4 rounds, or just turn tail and run. But either way the dragon is STILL in trouble. The rogue can no longer get through this without fear, nor can he get through this without taking damage, but it's still survivable 1 on 1.
Now, if the Dragon was fighting on home turf, with traps set up like floors doused with oil and such things, the 20th level character would have much more cause to fear, but could still win if backed up by an adventuring party worth its salt.