The lack of a windows phone app will have more to do with the small market share these phones have compared to IOS and Android alternatives than anything the Microsoft conspiracy gang are cranking out. However if there are large volumes of windows phone users playing destiny who want access to the the app it would only make sense for Bungie to oblige.
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What about the lack of Smartglass integration?
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Well, realistically it wouldn't take much effort for Bungie to even design an offline app for Windows or Windows Phone as they both can be developed using their existing HTML code. Furthermore, the code base can be universal (e.g. shared) between both a Windows 8.1 and Windows Phone 8.1 app; they would be identical, only the UI would need adjustments for the differences in screen resolution / size between a phone and a pc.
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Thank you for having a brain.