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Well JEE Mains percentile is surely better as it will help you in getting admission in the college all across the India whicle mht cet is sololy focused on colleges in Maharashtra. The college coming under mht cet will also be falling under JEE mains so getting a better percentile in JEE mains will surely be having a higher preference. Also the level of both the exams might be same but mht cet doesn't have negative marking which makes the things seems little bit more casual.
So getting a better percentile in JEE mains will always be provide you the better opportunities.
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