I really wouldn't like the job of fixing the problems with the first season, because to be honest I've had more fun in the free practice sessions chattin' shit and junk than in the few races I have attended, but that's not what you want for a championship...
If there was anything I would change it would be...
1. A later start time...but that is purely personal and wouldn't expect everybody to agree. At least I could race then.
2. Longer races. More chance to catch leaders or overtake.
3. Fixed Setups or setup sharing...already discussed.
4. Less emphasis on SC laps and more on racing.
5. Points for Free Practice attendance.
6. Less kneejerk reactions to problems... i.e. Changing the whole calendar because of one bad race...I was looking forward to Kyoto in the FBM