For some reason, the Bridgestones tend to do better in Indy than the Michelins, as evidenced by Ferrari's runaway 1-2. Jarno Trulli of Toyota (in Potenzas too) also took 4th place starting from the pits with a 1-stop strategy. Maybe he could have beaten Fisi to 3rd even, only if he had a better starting position.
As for team orders, I believe it shouldn't be done via radio, as the FIA are listening. I also don't know what Alonso was thinking in holding back his faster teammate.
IMO, Ferraris pace was unmatched the whole weekend. But if you would notice The midland cars were lapping faster than usual. This maybe due to Ferrari and Minardi being the only teams to run last year. But nevertheless its still a great team effort from Ferrari!