I have been teaching for both NEET and JEE (mains and advanced) for past 8 years. I will try to give a crisp and unbiased answer to your question.
If you look at the level of competition, it is very very high in both the exams.
Which means the struggle/ the effort a student has to put to get into a very good medical college or an IIT is almost equal.
POINT 1. (very important)
NEET is more of memory.
JEE is more of understanding.
Purpose of both the examinations is different. Therefore they must differ in their difficulty level.
Through JEE exams we have to select students with very good analytical and logical skills. Because they are future engineers or scientists.
Through NEET we select candidates who can become good doctors. A doctor needs more information, he has to be very fast in taking decisions and he should have great memory power. (hence we give less time to answer NEET)
IN TERMS OF DIFFICULTY IN GETTING INTO BEST INSTITUTES BOTH ARE TOUGH.
IN TERMS OF DIFFICULTY LEVEL OF QUESTIONS JEE TOUGH.