The Separation of Powers is an essential element of our Constitutional structure. It is designed to limit aggregation of power at the federal level at the expense of the people and to foster competition and a balancing mechanism among the three branches of government; the legislature, executive, and judiciary. Here is how it works: when Congress objects to an action (or inaction) by the executive, it can pass a law or withhold or increase an appropriation; the President can veto a bill passed by the Congress; Congress can with a 2/3rds vote override the President’s veto; the Supreme Court can hold a law passed by Congress and signed by the President unconstitutional; Congress can pass, and the President sign, a new law overriding the court’s decision; and so on and so forth. Therefore it should not be a surprise that, in recent times at least, the legislative and executive branches both fair better when they are in different party hands and thus freer to pursue their institutional Constitutional aims. Put another way, Obama may yet quietly celebrate the failure to attain a filibuster-free 60-vote Senate, and indeed at some point he may long for the divided government that saved Clinton's Presidency and that could have greatly benefited his successors.
The problem that dogged both Clinton (for the first two years) and Bush 43 (for the first 6) is that having both branches in the same party’s hands made it very difficult for either President to resist overreaching and overspending by their legislative partners. When Gingrich took over the House in l994, however, he was liberated to pursue his own agenda. He became master of his own house, took charge of what had been a very fragile beginning period of governance and developed an agenda that put him in charge of the government with, to his credit, many accomplishments--like welfare reform and spending restraint--that would have been near impossible otherwise.