Kerala University is comparably better than MG. It is better recognized in the industry. Other than this there are no such major differences between the two universities. The university offers decent academic sand placements. According to the recent highlights of Kerala University placements, students receive a median CTC of around INR 2.1 LPA.

Both Kerala University and MGU Kottayam are quite reputed. MG conducts examinations and publishes results in time. Their syllabus is also regularly updated. Other than that are no such major differences between the two universities. 

You can choose either of the two options based on your location preference. Thiruvananthapuram is better than Kottayam as a city. There are many good coaching institutes in the city.