Both are decent products. I prefer Juniper for the following reasons:
1) Cleaner separation of data plane from control plane. Higher end Cisco devices are better at this but most of the lower end products still seem to be more integrated than I like.
2) The Hierarchical config design means I can make changes only in areas that concern me without necessarily impacting other areas.
3) Easier rollback when one makes mistakes
4) I think there are less bugs/vulnerabilities in Junos vs IOS.
5) iOS has too many flavors leads to confusion with deployment.
One more advantage of junos over iOS. Juniper adheres closer to the standards than Cisco. Epigraph is nice, auto rp is cool, but with the less protocols in the standards it's much earlier to configure junos.