The biggest difference between Blackboard Portal and Quercus is usability. In the Winter 2018 term, a total of 43 courses were taught using Quercus with a total of 3250 students. The feedback was extraordinarily positive!
From a functionality perspective, the majority of the common features (file upload submission, quizzes, surveys, Turnitin, discussions, groups) exist in both systems. However, there are some differences. For instance, in Quercus there is no blog or journal functionality - however there are more flexible discussions or written assignment features that provide comparable assessment options. Same goes for quiz question types -- both system have the basic question types in common, but Quercus doesn't currently have hotspot questions although it does have an improved math formula question type.
For a complete overview of these features, please refer to: From Portal to Quercus: A Feature Comparison Chart
If you have any questions or would like to book a consultation to review your options, please contact us by email at: firstname.lastname@example.org