From the perspective of which degree you will obtain, the difference is insignificant. However, your study experience and student life will vary significantly depending on which home university you choose. Some important points to consider:
You will spend two of three course-based semesters at your home university
Tuition fees are 4000 CHF per semester if you choose USI as your home university
There maybe certain advantages for finding internships / jobs in the location in which you spend your last semester or thesis
At FAU, in the Computational engineering program, you have to choose your Technical Application Fields (TAF) giving you a different perspective in Computer Science and a deeper insight into engineering.
At FAU there are no tuition fees (for FAU based students)! Every student pays approximately EUR 127 per semester for student services and a basic semester ticket for public transportation, making it easier for the students financially.
To make the most of your studies the FAU provides academic, legal, psychological and career-based services to support the students and maintain their well-being.