So, to clarify, are you looking for a different 'load bar' type rack system, or are you looking for a 'tray' or 'rack' type system that sits on top of your OEM bars?
If you are planning on keeping your OEM rack/load bars then your options will be as limited as any other OEM generic load bar system. You can always put a universal rack on top, or something Frontier specific like the Heps Designs low profile rack. Basically any rack that is designed to mount to a variety of load bars.
If you are removing the OEM bars then the sky is the limit and you could put all sorts of things. Thule, Yakima, Rhino Rack. You could do a tower setup that with the specific rubber feet for our trucks, or you could do a track or channel type setup that you bolt or rivnut to the roof.