SEPARATION of powers - the formal division of governing authority among three constitutionally independent branches - is America's most striking governmental innovation and, on the whole, a most successful one. But major changes in the practical workings of separation of powers are posing new and troubling challenges. The confirmation hearings of Judge Clarence Thomas for a seat on the Supreme Court display these changes and challenges in high relief.For 26 of the last 38 years, a Republican president has faced a Democratic legislative majority. This condition is entirely without precedent. From 1789 to 1955, the same party or faction held the presidency and majorities in both houses of Congress for all but 38 years. Until recently, the constitutionally inspired rivalry between Congress and the president was curbed by the practical political cooperation encouraged by unified party control. Now, divided control heightens and distorts the old institutional conflict. The Constitution says the president "shall nominate, and by and with the advice and consent of the senate, shall appoint ... judges of the supreme court...." Through most of US history, the Senate has seen the choice of a Supreme Court justice as basically the president's, and limited its own role to catching "mistakes rejecting the occasional nominee who was unqualified for the highest judicial office by reasons of character or ability. But the Senate's role is now being drastically changed. It's not just that a Democratic Senate is reviewing Republican nominees, but that both sides consider divided government as a natural part of contemporary politics. The GOP would like to win congressional majorities in 1992, but it really doesn't expect to; and while the Democrats want to see one of their own elected president, they are resigned to waiting at least four more years. The US now has two governing parties, not one; and each seeks to max imize the reach of the institution it controls. Appointments like Thomas's become battlegrounds. Many Senate Democrats are torn between the traditional view that he who wins the White House gets to put his people on the court - and the new recognition that following the old system means the acquiescence of the Democratic legislature to total Republican policy control of the judiciary. No one doubts that Clarence Thomas is a man of high character and great ability, an example of much which is best in our nation's traditions. His one "fault" is that he is a conservative Republican. Senate Democrats can't directly offer that as ground for his rejection, of course, so they must pretend that there is something unacceptable by constitutional standards in his views. One of the results this time was the endless questioning of the nominee's views on the role of "natural law" in constitutional adjudication. On the other side, Republicans, sensing the Democrats' discomfort over the tensions between the old norms and their own practical political interests, have set upon a course that may help get nominees confirmed but which can only confuse the public. Nominees are now coached to smile, be deferential - and obfuscate as much as possible. Thomas spent much of his five days of testimony running away from the force of the ideas and understandings which have informed his political life. But it's not hard to see why he did this, since the Democrats' strategy was, in effect, to find a way of making him appear "guilty" of holding to views which are simply Republican and conservative. And it's not hard to see why the Democrats have responded as they have, since in this age of divided government, they are seeing the federal courts come under full Republican control. We could end this discomfort by restoring the United States to unified party control - giving one side a chance to govern for a time, and then turning to the other. But we show no signs of facing up to the many tensions and confusions inherent in divided government.