We have OLD Nautilus and fairly new Cybex at the gym now. Of course, there is no comparison since the Nautilus is pretty ancient. I really like the Cybex - we have some regular, some Eagle. It is very smooth and fluid, most of the machines are pretty self explanatory or have great cues given on the machine.
I am sure the newer Nautilus is much better than what we've got. The old stuff isn't bad, just not as updated at the Cybex (ie: to add weight in between the stack weights, you have to use little free weight bars instead of having that feature 'built-in' like the Cybex).
The girls that chose the Cybex did A LOT of research at several different gyms and trade shows, and they liked that the best - but I do not know all of their reasonings behind that.
Good luck with your decision.