The Mariner carries 30% more passengers than the Navigator (700 vs. 490), but the individual suites are about 15% larger on Navigator (301 sq.ft. vs. 356 sq.ft.). The real downer IMHO is most baths on the Mariner lack the separate shower found on Navigator (and Voyager, incidentally), and the tubs are high and deep, making them difficult to get in and out of. In addition, the tubs have a low "overhead", causing tall people (like me - 6'2") to learn to "shower while crouching". To RSSC’s credit, they have recognized this issue and have converted some of the tubs to walk-in showers.
One real advantage is the two additional restaurants available on Mariner: Signatures and Latitudes. On an Alaska cruise during its inaugural season (2001), my wife and I had a truly outstanding meal in Signatures, one of the best meals we've ever had, afloat or ashore. That's a real accomplishment, as we've enjoyed a couple of Michelin 3 star restaurants in Paris, and some of the best places in the states as well.
We’ve sailed in both ships twice, and are booked for two more cruises in Mariner this fall – Singapore to Sydney and then Auckland to LA. We like both ships, probably with a slight nod to Mariner. You won’t go wrong on either, or on the Voyager either, for that matter.