Basically EE take the PDF of a print magazine, wrap an app around it, and sell it in the App Store. The do not use the text from the print magazine, nor do they use whatever extra media a magazine might have. No, they just take the scanned page PDF and call it quits. The digital magazines they make are pretty much unusable on my iPod Touch.
There are a bunch of things EE could be doing. I'm going to limit it just to 3.
Before you make an app you should look at every single piece of digital content you have. This is your source material for the app, not just the printed contents of the magazine.
One of the magazines converted by EE is Dazed, an UK based "fashion, art, film, music" magazine. I checked the Dazed website, and the contrast between the website and the app is astounding. Dazed have videos, photo galleries, and all sorts of content on their website that could be in the app. I'm a little shocked that the app is a magazine and not a media app.
People read text, not images
I've downloaded 4 different titles converted by Exact Editions, and the text is unintelligible until I zoom in 4 or more times. Yes, the page images are great, but if you want me to read the words then you have to give me text. It's wrong to expect me to read an image. You _look_ at images and _read_ text.
There is also a third problem, and I've seen this in all their apps. Each page takes too long to focus. This is a coding problem, not design, but it should have been fixed before the app was released. At the very least I need to be able to swipe a page turn while the page image is still being sharpened. What if I don't want to read a particular page and just want to skip past it?
I think I'm going to leave it there, but I can give you one more tip. Go download the GQ app from last fall (October, for example). This app does many, many things right. Study it and see what parts of the design that you can copy.
P.S. If you know someone working on a magazine app please send them a link to this post. I'd like to work with them. Each poorly designed digital magazine is a lost opportunity. Readers will try it and some will decide that apps just don't work. Good luck with changing their mind.