Any reason not to set up Exchange 2013 with the iApp?

I always recommend using the latest version of the iApp. Even if you need to make a few modifications after the iApp is deployed it will build a baseline for you and significantly reduce your deployment times.

I have not run across any reasons with my customers on why the Exchange 2013 iApp would be an issue. The iApp itself offers several deployment models to fit your particular deployment.

Note, if you're going to use MAPI over HTTP there are a few configurations you'll have to build by hand but those are documented in the deployment guide.

Cody