Yeah - I agree. It's very frustrating since I sold my iPad and just carry an iPhone and rMBP. Why on earth would anyone buy books through iBooks instead of Amazon/Kindle? Much bigger selection and you can read your books on Mac, PC, Web, Kindle, iPhone/iPad, Android, etc. 10.9 should help a bit.
For magazines, I go with Zinio for same reason, although the current Mac reader totally sucks (which their tech support agrees with...).
I actually hate all of these proprietary book/magazine formats. Company goes under or just decides to shut down the service and all your content you paid for goes poof

Some magazines are still available in PDF, which is the most portable - it's even in the name
Music companies finally gave up on DRM and video mostly, but the "print" vendors are being stubborn.