I don't know of an app that will do exactly what you want, but you could take a standard learning app, set a timer when he starts, and not tell him how to exit the app. Once he has played with the app for a while and gets bored, you can exit it for him, set a timer for the appropriate amount of time, and let him watch netflix or play games. You could do that with pretty much any iPad app, but here is one example: http://www.148apps.com/app/384334005/
That said, I'm not sure that's the best approach, as it may teach your son that learning is a chore, and can't be fun. If you want to use an iPad app, I'd encourage you to find one that your son actually enjoys using, so he can learn letters or numbers and be playing games at the same time!
Better still would be for you to sit down with him while he does the work, if you have time for it. That way he can learn to enjoy learning, reading, and math because it's associated with having time with his dad. Granted you will have to relax and enjoy it yourself, so that it's an all around positive experience for him.
For letters and reading, I have had good luck with the Kumon workbook series. In particular, I've used their uppercase letters, lowercase letters, rhyming words, and rhyming words and phrases workbooks successfully, by the end of which the child is ready to sound out words and start simple reading and writing.
If you use these, be careful not to overload the child or to get frustrated because you think the child can do better. A page or two a day may seem slow, but it will have him ready to start reading in less than a year. Also, do read the instructions, especially the parts about what sounds the child should make while tracing the letters.