This is a question that is difficult to answer. With that said, I would say that the most intellectual religion in the world today is Christianity for several reasons.
First, Christianity has been around for a long time. For this reason, there has been much reflection and study. Many of our best universities have been started by Christians for the study of Christian theology.
Second, Christianity also encompasses much of Judaism, which actually predates Christianity and is also very intellectual. From one perspective, Christianity has taken some of the best intellectual fruits of Judaism.
Third, Christianity has shaped the modern world - even from a global perspective.
The question is sensitive as any answer it likely to evoke emotional responses. However as the answer above equates intellectuality of a religion with its antiquity, I would like to point out that among all the major religions of the world today, Hinduism has been around for the longest.
Further, I suggest that the intellectual level of a religion should be judged on the basis of how a religion accepts new ideas, rather than how old its origin are. This at times also amounts to religious tolerance.
Religious practice of denouncing other religions and those who do not believe in one's religion is, or calling one's religion better that those of others is, in itself, a sign of religious intolerance.