Jipmer has only 160 seats for people outside puducherry and from that only 50 for gen category. Neet has about 26,000 mbbs seats in total(gov).
On the other hand jipmer paper is comparitively easier. Also not many students appear in jipmer as compared to neet.
But taking everything into scene, neet is a better exam and with proper effort you can get into a good mbbs college through neet. Jipmer is a singular college that not comes under MCI so they have complete freedom from the government in every respect.
If you prepare for neet, you dont have to worry about jipmer( the english and logical analysis questions are to be studied seperately as they only come in jipmer).
Hope that helps!!! 🙂