I don't offhand know where there's a side-by-side comparison, but on most hardware specs the One wins: higher screen resolution, more storage (but see below), more powerful cpu, and IMO better camera. But as you say, the Nexus is already stock and much cheaper.
There was a rumour recently that a 32GB, officially LTE-enabled N4 might be announced at Google IO. As that's only next week, you might want to wait to see whether that's true before pulling the trigger on the Nexus. If it does turn out to be true, even if you decide the 16GB is enough it would probably drop in price (as happened when the N7 went from 8 or 16 to 16 or 32).
as this is slightly off topic, feel free to move to an appropriate thread if you like