Hello Candidate,

It's a really tough question to answer probably because both universities are best in their own ways. I can only compare both universities so that we might a conclusion.

--> JNTU-HYD was established in the year 1972. It has an A grade accredited by NAAC.
--> Osmania University was established way back in the year 1918. OU has been awarded 5-star rating by NAAC.
--> The question paper from JNTU is of 4 set type question paper. Students are allowed to write the exam in their own college due to these 4 different set of question paper which doesn't allow copying in the exam as no two students will have the same questions in their question paper.
--> While Osmania University follows a single set question paper. Students are allotted with centers with students need to go for other colleges to write an exam. By doing this copying will not happen as the student is aware that the faculty is new and they are not their college faculty just in case like JNTU colleges.
--> JNTU-HYD has more than 200 colleges affiliated under it.
--> OU has hardly 7 colleges under its affiliation.
--> In JNTU-HYD If a student secures more than 70% it's awarded the highest grade i.e A+.
--> In OU a student can get easily around 85-90%.
--> The syllabus pattern of JNTU-HYD changes every 2 years with proper effect on subjects which keep on changing according to each regulation batch joining. Mostly the JNTU syllabus keeps on getting upgraded with the latest topics.
--> OU syllabus changes hardly one in a while say 10 years. The students have to follow the same old textbooks with the same old syllabus.

These are major differences of JNTU-HYD and OU. It's similar even if you study in Universities or affiliated colleges under these universities. You won't find mind much difference. As I have listed the pros and cons of both these universities. So, you decide what would be best for you.
All the best.