Run it or run it well?
I still don't have all the 3.x rules down and I think that when people criticize D&D as being too rules heavy that they have a point. I don't agree with them, but I think they have a point.
IMHO, when you are new to the system, you should playtest a combat and some of the wackier rules that go along with the setting. For example, in Shadowrun, I would playtest a combat, decking, and spellcasting. These playtests should not "count" as part of the adventure. You're just shaking out the rules.
Along similar lines, I think that core books without adventures included should never rate higher than a B (4/5, 80%) even if the rest of the game is perfect. The whole point of introductory adventures is to help the game master as much as the players. No intro adventure and you are essentally telling the game master "This game is so great, if you have problems running it, then you are the moron, not me".
... but I digress ...