My company wants to build a custom, native iOS app for iPad. "Custom" because this will enable us to add bells and whistles that are not readily available within Salesforce1. However, the ability to determine which fields appear on the app via server-side config is a pro for Salesforce1. This would enable us to avoid having to re-distribute the client upon layout changes. Is it possible to get the best of both worlds within a custom app? What approaches should I be considering?
I would seriously consider using "Field Sets" to control the fields server-side. I'd personally set up one per object for display, one per object for query/search, and anything else you are looking to build into your app (you can also specify additional Field Sets per profile, if desired, with a Custom Setting denoting which Field Set applies to their profile)