It's simple enough to envision another governing body that is structured much differently and funded much differently being more successful at getting the correct information to levy the correct punishment. Granted, you and I could probably be more successful. Yahoo's already shown that they are more successful. Once you have the organization in place, then you work on the stupid rules. A little common sense goes a long way in that area.
The NCAA's primary problem is that the small schools and big schools have very different cares. There are rules written in that are passed because D3 schools want it but it's contrary to anything the big schools want. Some of the big nagging issues that have come up this year - like agents, autograph fees, player likeness, etc - those simply aren't a concern to schools outside the BCS.
No amount of rules are going to make those things go away. There is huge money at stake and players are going to find a way to get some. Small schools feel like eliminating or softening those rules would provide a competitive disadvantage to them (and they would) but results in a feckless NCAA because there is really no way to enforce them. Schools can't do it. The NCAA can't do it.
And while you can call them "stupid rules" (and they probably are), they were passed because every single NCAA member-institution gets the same vote. If one little school hears that another little school is providing milk and cookies to recruits and they (like many of their fellow schools) can't afford to compete, they propose a rule. A spinoff fixes a lot of these issues because the FBS schools don't really need a limit on such things and it costs them more money to comply and make sure no boosters hand out milk or cookies than it does just to buy the damn things.
A breakaway will probably streamline the rules to the point that things at least make sense for the money involved. It will also mean that money for the governing body won't be used investigating D3 issues. It won't be perfect still but it will be a helluva lot better.