In short, Obama thinks Citizens United was "devastating" (as he called it a few days after the case was decided) because it freed his opponents to criticize him and interfered with business as usual in Washington. Many Americans would see those as advantages. In any case, it's clear that Obama views campaign finance regulation as a way of managing the political debate and keeping it from becoming too "extremist," a rationale the court has never endorsed and one that is totally at odds with the First Amendment's command that Congress "shall make no law ... abridging the freedom of speech."
Similarly, the editorial board of The New York Times, which decries "the distorting power of money on American elections," cites the "broad ideological change" sought by "the Koch brothers" as a reason to keep the aggregate caps on campaign contributions. "To equate the ability of billionaires to buy elections with 'freedom of speech' is totally absurd," Rep. Bernie Sanders, I-Vt., opines, while Sen. John McCain, R-Ariz., bemoans "the undue influence of special interests" and Rep. Nancy Pelosi, D-Calif., complains that "the Supreme Court has chosen to pour even more money into our process and our politics."
As self-financed candidates periodically discover, you cannot really "buy elections." Even if a candidate is interested only in gaining and retaining power, he has to convince voters he is worthy of their trust. The "undue influence" that worries Breyer, Obama, Sanders, McCain and Pelosi is ultimately based on the power of speech to persuade, a power Congress is forbidden to regulate.