Gifu University has a flat terrain and does not need to go up and down the mountain.
There are many cities around Nagoya. It takes less than an hour to get to downtown Nagoya by JR Alpine Line, which is not too far.
Whether the university itself is good or not is a matter of opinion, at least in central Japan.
If you want to work, the countryside in Gifu is certainly not as good as Osaka in Tokyo, but the learning environment is much better than the colorful world in downtown Tokyo.
Decide your future, not your life.