If your prime tenant is SU you can't stick it out in a pasture in Lysander, Van Buren, Camilus, Onondaga, or Manlius. You have to be reasonable.
I personally think that the location was picked to help kickstart some urban redevelopment in the center city and keep the facility as close to the University, and extend it's reach, and center city as possible. There was your mutual benefit there.
The University wins by freeing up acreage in the heart of campus, having the stadium within site of campus, and a new facility.
Cuomo and Mahoney benefit by bringing a big project to Onondaga County that can be seen as benefiting the city without any contribution from the city in terms of financing, targeting the project to renew a section of the center city instead of placing in more obvious areas such as the inner harbor, which would be seen as a sop to Congel and Destiny or South Campus, which would create resentment that the government was underwriting a purely SU facility.
Fans win because it would be a new stadium, but it still wouldn't address some key issues such as parking, tailgaiting (it would make it worse if that is even possible), and ease of access, at least without substantial improvements and change in the area. It's obviously a tight squeeze and you are going to need to significantly change the surrounding area to provide parking adjacent to the facility.
I think the better choice is the inner harbor because of the stadium, Destiny, and the development around the harbor would reinforce each other, it also the best choice from an existing traffic and infrastructure (would allow for a fan experience similar to other football stadiums) perspective and least disruptive and most additive to the city and county as a whole.