I agree that soccer should be a part of the Olympics, since it is the world's favorite sport. But in it's current state I don't think it's worth the trouble. It's basically just a U-23 tournament with a few exceptions. The same can sort of be said for baseball.
I think the IOC should pass a rule maintaining that unless a governing body (in this case FIFA) allows countries to send their best athletes, that sport is out. This would maintain basketball, softball and women's soccer, but effectively eliminate men's soccer and baseball from Olympic competition. The men's World Cup would thus maintain it's stature, and the fledgling World Baseball Classic would gain a big boost in global prestige.
What's wrong with a grand U-23 tournament? Was it wrong that the Games never allowed professional athletes until recently? Does that diminish the accomplishments of, well, every medal ever won in sports with professional competitions and leagues? I understand that the Olympics is hamstrung because FIFA makes billions on the World Cup. But that doesn't tarnish the Olympics for me. Nor does it for the Brazilians, Argentinians, Nigerians, etc (hell, even some of us here in the U.S.A.) who will follow their team this month.
This is where Money has corrupted sports and it's participants. Soccer should in the Olympics and it should be bigger than the World Cup because it is on the grandest stage--The Olympic Games.
The rule should be simple--The best players from each country represent their country's team in the Olympics. I mean come on it's only every four years. Ridiculous!