Gran Turismo's only
flaws are not caused by
bad programming, but by
lawyers.
The lack of car damage mentioned by xmatt above is due to the reluctance of some car manufacturers to see their products get wrecked during game play--especially if realistic costs of repair are also implemented. This is also why the only reason to pit in on the longer races is to get your tires changed.
Another flaw is the lack of availability of some cars, and a glut of others. Lambourghinis, Ferraris, McLarens, and Porsches are nowhere to be found in the game, because these companies signed exclusive agreements with Electronic Arts and other companies for their vehicles to be modelled. Amusingly, you can buy cars from RUF, the "car company" that buys Porsche automobiles, then does enough tuning and parts replacement that the result is, technically to the German Government, a separate brand of car.
Less explicable are the lack of key models from brands that already exist in the game. Why did BMW only allow their 328i model in the game, and not the Z3 Roadster? Why didn't Volkswagen let any of their Jettas in? I would gladly have traded the access to 10 different models of the Mitsubishi Evolution or the Nissan Skyline for just one of these cars.
Despite these flaws, GT3 is still a great game, and a must for anyone who owns a Playstation 2. If you don't own a PS2, I recommend doing what I did and buying the pack that bundles GT3 with the console.