I wish aqueducts had buildings so they wouldn't be degraded to this simple one-time decision. I wish they were more interesting, than anything...
But as for what I chose, when I do build them, it's for that IZ adjacency. I'm usually not someone who obsesses over optimization though- I don't like chopping and I hate to see the yields of floodplains be crushed by dams. The only time I really obsess over it is when I'm playing someone like Germany or Japan where you're actively encouraged to go nuts about every single point of adjacency.