Its the Riders as Well as the Teams
To second your comments, I add that Vermullion (sp?) was racing on his home track, and that Stephan Chambon, who most consider to the the stronger of the 2-man Suzuki squad was still recovering from broken ribs (and, if I recall, broken ankle) that kept him out of round one.
In addition, even though these bikes are supposedly "production," the construction and setup is at least as important as for Superbike. Honda always have the strongest support teams and the biggest budgets.
I am not at all knocking Honda for this -- an old acquaintance of mine is team manager for one of the AMA factory teams, and I know how good he is. My point is that ALL the bikes at the front of the grid are a lot better than what you could buy (that is, assuming that Honda actually had any bikes to sell you, but that is another issue).
Buz, step in and kick me too, while you are at it!
Bob