Nagoya isn't as bad as people make out, it's just has a bit of a different focus to a lot of other Japanese cities. My suggestions would be:

Nagoya City Science Museum - one of the best science museums I've ever visited
Toyota Museum - high quality car museum, very well selected non Toyota stuff (the only place I've seen a Duesenberg for example)
Toyota commemorative museum of Industry and Technology - hands on museum with working exihbits tracking Toyota's life from the looms through to car production
Toyota factory tour - has to be organised ahead of time but really interesting
SC Maglev and Railway park - reasonably new rail museum, a lot of exhibits and some interesting stuff on the maglev
Tokugawa art museum - not a huge museum some nice stuff
Inuyama castle - one of the best castles in Japan
Ukai Fishing - The night fishing at Gifu is one of the highlights of all my trips to Japan
Day trip to Kiso Valley - in particular the walk between the well preserved postal towns Tsumago and Magome

Nagoya is an industrial city so a lot of the attractions are geared around science and technology rather than temples and geishas. I think a lot of people see that as a weakness but personally this is why I enjoy the city as it's a very good counterpoint to the Kyoto's and Takayama's.