Jefferson was a small R republican first and foremost (politically speaking). He can be said to be a "federalist" in only the broadest sense of the word. Of course, all of the leading lights of the founding generation would be shocked by the immense power now invested in the central national government.
Jefferson was also a little too smitten with the "romance" of the French Revolution, probably mostly due to his strong aversion to the English nobility, and nobility in general.