>Are they mismanaged?
Some are, some aren't. Normally mismanaged firms don't last in the free market but the government has a habit of giving out bailouts every so often which distorts this.
>Are these oligopolies natural?
Yes and no. In the free market there would be some demand for the existence of larger investment banks, because such firms would be seen as more reputable and more stable. So in the sense that big banks would exist there would be an "oligopoly." However, through licensing requirements and various other regulations the supply of large banks currently artificially restricted by the government, so it would undoubtedly be less of an oligopoly than is seen now. Further, it wouldn't be a true, textbook-definition oligopoly in either case, because those large firms aren't the only firms in the market. There would still be thousands of local and regional banks competing with them.
>how do we go about deconstructing them and making the economy more efficient
For any given business, industry, or sector of the market, the answer is always going to be to limit government interference within that area as much as possible. Eliminate licensing requirements, cut out the red tape and regulations, and allow the free market to do what it does best.