If you have multiple windows open in the Java application, try minimising all except the one you want to interact with. This will reduce the amount of elements Blue Prism has to read to match your element.
Try manually minimising first then you can a...
Are they quicker or slower after the upgrade to 2016?
I would, where possible, avoid using spied elements and screen interaction for Excel - and instead use code stages such as those in the Excel VBO.
Are you using a queue to manage your work items? The Foundation guide and Work Queues guide will be helpful. Use the Mark as Exception stage on the work item, then Get Next Item.