if the price is the same, go with the rubicon. the only thing special about the sahara, as opposed to an x or a sport, is that the fenders match the paint. the rubicon, on the other hand, will come with lockers (electronic), bigger axles (dana 44's i think), disconnecting swaybar (you can disconnect it with the push of a button), and a tranfer case with higher ratios. if you plan on building it yourself, you can probably get all those extras for much cheaper, in which case i would say go with the sahara (assuming that the rubicon is more expensive).
when i bought my jeep, i knew i was going to completely overhaul every system on it, so i went with the one that had the lowest mileage. the only thing stock on my jeep is the motor and tranny...and the tub.