The tarrasque has always been a bit of a problem. It's supposed to be the Ultimate Monster, the combat brute to end all combat brutes... but long before you're tough enough to take it on hand-to-hand, you can fly pretty much at will, which ends its ability to pose an offensive threat to the PCs. As it stands, killing the tarrasque is an exercise in character sheet math: How can we deal more than 40 points of damage per round over a sufficiently long duration (or attack in some other fashion, such as ability drain) to bring it down?
Making flight harder to come by will help, but remember that this is a beast you don't expect to fight until epic levels. If at-will flight is possible ever, you'll have it by the time you face the tarrasque.
I really see no way around it; the tarrasque needs either wings of its own, or a ranged attack of some kind. I'd give it an "Earthshaking Roar" ability that inflicts AoE sonic damage and knocks flyers out of the sky. Give it that, along with combat stats suitable for an epic-level solo brute, and killing the tarrasque will become a deed truly worthy of the name.