The sad (?) truth is that features are often prioritised over qualities. This is, in part, a result of not describing qualities in terms of their impact on features and vice versa. In my experience, though, it's usually due to the prioritisation process not having any representation other than end users. Everyone is a stakeholder and it's one of the architect's responsibilities to speak up for the technical qualities.

Jira can help here. By attaching templates to specific types of items you can remind developers and analysts of the non-functional aspects they should consider before starting implementation.