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I'd thought along these lines: 5 heats of 50 riders in a mini race format, top 15 or so progress to the main race with the grid positions still being determined by the riders fastest lap but I think @B0N0R nailed it; qualifiers were sketchy enough without being in a close bunch with inexperienced riders.
I really feel that the crashes were down to rider error, certainly the ones I saw, not due to course design/road surface etc
One format possible would be 'race to qualify' in which riders would be sorted into random qualifying groups, maybe with the seeded riders spread between them, and have to race thier way into the main event. This would mean that the new riders get some race experience even if they don't qualify, and spectators get to see loads of racing. It would also remove the disadvantage of being in a slower qualifying group.