Solve subscriptions. This is what the apps do. Adobe DPS, which I mention below, is so totally geared to creating paid subscription content.
The Readability fiasco was unfortunate since I'd like to see other non-ad based approaches to paying open content publishers/creators. Unfortunately, no one on the vested interest side of the fence (including Apple) has any real motivation to solve for this.
+ Background Updating
+ Push Notifications
+ Works offline, always
+ Doesn't go down when your server does
+ Subscriptions without a credit card.
I think all of these are something that mobile browsers can't do at all.
It can be clunky in places and I've seen terrible magazine apps created with it, but that can be said for native apps as well. There is the Adobe creative cloud price to factor in, but if you are doing anything with creative cloud already, you have access to this.
As for actually getting into the actual iOS newsstand as a magazine, that I'm not clear about. I have the impression that Apple has tight relationships with legacy magazine publishers and gives them priority.
I think the bigger issue, besides pricing, is content lock-in, as you note. I've seen some other systems (not Baker, I'll check that out) that offer "free" app wrappers for magazine style content but tightly control the creation process as a lock in mechanism (and I'm not even referring to Apple here).
Curious: are you actually publishing to newsstand or standard apps? I'm wondering what the barrier to entry to the newsstand is in terms of approval vs. apps. At least with ebooks, it gets weird quickly on Apple's end (long long approval times for independent publishers unless you go through an "approved" broker, etc.).
We publish a standard app at the moment, because Baker did not support Newsstand until a short time ago. We will be updating in the next week or so.
DPS pricing is still bad. Single edition only gets you one issue. One freaking issue! You need to upgrade to professional ($495 per month!) or above to publish multiple issues, and then pay $.30 every time someone downloads one of your issues. Compare that to setting up Baker (free) and setting up Amazon S3 free account (15GB data out per month) and DPS looks like a total scam.
They do have a good reach and that will definitely help them, but the tablet market is now big enough for multiple players.
Systems like newsstand and Google currents seem nice because of their ui/ux, but that's only because its so hard to compete with such giants that have relationships with giant content creators who want surgical grade DRM.
In this case, a website works perfectly well, with the advantages of being searchable and sharable in far more granular and broader formats than an app, thanks to the likes of Google, likes/retweets etc.
No, it's a conflation of the desire to publish with the desire to target the best electronic devices for reading (tablets), with the best format for _each_ platform (native), with easy 1-click access to monetization (already stored credit cards and people known to buy things).
None of the above are solved by a website.
And much less it solves stuff like background updates, large volumes of data and pictures being readable offline, etc.