I have taken such things into account. I revised the system after some reworking of the numbers.

You are forgetting that Great Wyrms are strategic geniuses in the field of battle.
Unfortunately, a GM may not be. It comes down to the strategic genius of the player against the dragon. The player might very well win do to vastly supperior knowledge of his own capacity.
Not likely. This Great Wyrm Red Dragon may seem a match for that one character, but the Great Wyrm could actually take on four such characters just as easily. (Actually, a normal party would be pretty easy, although four Level 44 Fighters might do the trick.) Fast Healing will make little difference when you're taking 78 points of damage PER ROUND; damage reduction won't make a difference at all because the Great Wyrm could bypass is EASILY; evergy resistance might protect against the breath weapon, but not against the pphysical attacks and crush; other magical items will make little difference.
Fast Healing will make a minor differance, it is more important after battle, as it completely eliminates the need for after battle healing spells.
However, the DR DOES make a differance. The Red dragon's bith deals 35 or so average damage, most of the other attacks deal less. Every feat reduces this by 10%, thus three feats could easily drop the damage per a round to 1/2 normal!!!
As for crush, Legendary Wrestler goes a long way, though they may not escape easily, a intelligent party should avoid getting all nailed by a crush at the same time. It is however one of the more devestating tactics.
The problem is that a 44th level Figther with a relitively dry weapon is dishing back about 100 damage to the dragon per a round.
With the dragon hitting with its breath weapon it isn't even, they are dealing the same back and forth with the same HP. Plus the fact that the figher may be hit by a mass heal.
Epic Feats are a MAJOR power progression. They should not be underestimated in their power to completely trump a creature.
Level = EPR in my system for all normal characters. I bumped up NPC wealth to keep them on par with PCs. (Not quite, but close. NPCs have 50% the wealth of an equal PC.)
It is good you seperated them.