Are reports available that display all instances information together? For example, is it possible to get a report or something similar that shows Instances with Highest Wait Time like is on the first page, but for a longer period of time such as a quarter or year?
If not, are there any reports the can be used to look at all instances to compare changes over time between instances?
Each report is run against an instance. You can run the same report against multiple instances, but you'll have to collate the data manually.
One thing you can try is to create a group on the dashboard of instances you want to compare. When you click on the group level, it will show relative information about all of the instances contained in that group.
Not exactly what you are asking for, but you can see if that gets you closer to what you want.