Kuriowa Sensei wrote a great article on this:
I would advocate that you must first learn shape (kata), then how to express shape naturally (waza); The difference between kihon waza and nagare waza would simply be the appearance of the technique. Kihon waza would more closely resemble kata while nagare waza would have a more organic appearance.
I would also advocate that if you cannot perform kihon waza, then you cannot perform nagare waza. In aikido we sometimes skip kihon waza because its "hard" - uke hunkers down and the muscling begins. Do not fault kihon waza because of poor uke waza. Similarly we tend to push nagare waza because its "softer" - uke maybe complies or over extends. Again, do not fault nagare waza for poor uke waza.
Either way, the point I am getting at is our perceptions of kihon waza and nagare waza are flavored by our ukes.