obsi,
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Using an application such as
TouchControl will allow you to effectively duplicate the Pronto interface, but the iPad does not have many hard buttons. TouchControl could talk to the RFX9600. You would probably want to use some JavaScript to improve your programming productivity. Unfortunately, there is no IR library.
I have no experience with Keene, I have been using Global Caché units. While it would be an interesting, not very difficult, intellectual challange to talk to the RFX9600, I'm very satisfied with the GC units and GC offers some small interface boxes that can be tucked away in corners. And, the GC units don't have the little timing glitchs that you'll bump into using the RFX9600.