Do we still have separation of powers between Congress and the President? Or do they now work together more than separately?
(This is not about party domination--consider separation of powers since the Watergate era.)
I would say that there is still a separation of powers evident between the Executive and Legislative branches of government. I think that the concept of "working together" or "working separately" does not really indicate the presence of separation of powers. Both branches can be separate from one another and still work together. The Health Care legislation might be one example of this. While nearly everyone involved left the discussions and the debates not fully getting what they wanted, it was evident that both sides worked together to accomplish some form of legislation. That being said, neither side was fully able to bully the other side. The President wanted something to be passed, and Congress drafted legislation for it. There was little convergence or blurring of duties. They did hold divergent views on the issue, but there was a distinct handling of responsibilities in being able to bring legislation into law, proving the presence of separation of powers. We can also see this in other examples, such as in 1994 when then President Clinton had to recognize that his power was being challenged by a Republican Congress. In the end, I don't think that the principle of separation of powers has dissipated, but rather become more pronounced over time.
We most definitely still have separation of powers between Congress and the Presidency. This is sometimes more obvious and sometimes less, but it is clearly there.
For example, during this administration, President Obama has not been able to get what he has wanted in terms of an energy bill and was not really able to get the health care program he wanted. This was because of resistance from various parts of Congress.
Similarly, President George W. Bush was not able to change Social Security the way he wanted to (by encouraging private accounts). He was also unable to get the immigration reform bill that he wanted.
Congress is by no means willing to roll over and let the president do what he wants.