This was on again the other night, so I watched it for the 100th time. I think I agree that Fugit was fine. He's an awkward 17 year old playing an awkward 15 year old. If he was smooth, it would be a little weird. In the bigger moments ("I AM THE ENEMY" and "I LOVED HER"), he's not great, but in the quieter moments, I think he plays the wide eyed kid well.
I do disagree on the Crudup/Pitt thing. I think with Pitt, it's a different movie, and the whole movie would be imbalanced. That kind of super wattage would take away from the movie. The strength of the movie is the scruffiness of it with smaller actors reflecting the level of the band who isn't quite there yet. It would have made more money, but I don't think it would feel as casual or rewatchable.
I do want to add one thing. Every time I watch it, I love Jason Lee more. He's such a charismatic and fun performer ("actually, THAT you can print"). He had a fine career and is beloved by men of a certain age, but I wish he had more shots like this.