The answer depends on your preference of college as both the exams have their own importance.  JEE Mains is conducted by Central Government whereas NATA is conducted by Council of Architecture. The institutes that give admission on the basis of JEE Mains paper 2 are NIT'sand GFTI's(Government Funded technical Institutes) whereas by NATA you get admission into Private colleges and State level colleges, other than NITs and IITs. Jee mains paper 2 gives chance to join at national level colleges and NATA exam helps to join at state level colleges. This difference can be simply indicated as difference between state level(NATA) and central level exams(JEE).