The UN is full of flaws, I don't disagree, but there is no yet any other international organization that parallels it. It would be practically impossible to find alternatives for the UN's branches: UNDP, UNESCO, FAO, etc.
And concerning the power of small nations in the UN, the Security Council surely does not allow that to prevail if any policy goes against the interests of even one member of the Council. Russia did use that power extensively. Many people argue that Africa should be given a place in too, given that it is such a huge continent rigged with most of the world's problems of famine, poverty, malnutrition, corruption, miscreant states, etc. But yes, it cannot be denied that the Security Council is vital for the proper functioning of the UN (prerogative which the League of Nations did not provide, and can be traced to it's downfall).
With the superpowers' positions changing on the world map, it's inevitable that the Security Council will have to undergo changes too. Perhaps an alternative to the 'balance of power' theory? But like Borakk drew out, it is unlikely for superpowers to think of countries below them.
There may be other organisations that are more useless than the UN. What about the Olympic Games? Don't athletes and countries there waste more money than the UN does? The FIFA? The colossal salaries of sportsmen? The EU, which is already set on a downfall? The NAFTA? Those economic blocs preventing food prices from falling down just to protect their own farmers, eventually taking away the fishing rod of poorer nations? Any other organisation?