These resources and ideas were created for a classroom where you have a class set (or enough for 1/stand) of iPads that you cannot add apps to. These ideas can of course be adapted for use in a 1-to-1 setting.
Note Reading: MusicTheory.Net (Free)
MusicTheory.net is a GREAT website for drilling music theory (note reading, interval itentification, etc.). You do not need to download their app, it works in Safari on iPads. When you create a customized exercise you will get a permanent link to that exercise. I've found that the easiest way to direct students to the correct exercise is to put buttons on my school orchestra website.
Noteflight Learn ($69/year)
NoteFlight Learn allows you to create a NoteFlight Website where users can browse scores that you create and post to your site. I use this for things such as rhythm studies and sight reading. If you would like a temporary username/password to view my NoteFlight Website, contact me here and I will send you some login information.
I prefer this to printing and copying rhythm studies/technique exercies because when I inevitably make a mistake, I can quickly correct the mistake and students will only need to refresh the page to update. And no waiting in line at the copier that will probably get jammed or be out of ink!
Keynote Live (Free, if you already have the Keynote software)
Apple added a new feature to their Keynote program recently called Keynote Live. It allows you to broadcast your Keynote slideshow over the web. Students just need the link to get the slideshow up on their iPad screen (using Safari-they do not need to have the Keynote app downloaded to their device). I have used it for sight reading exercises because it keeps students from being able to write in note names, a habit I am determined for my students to break this year!