I'm with you, but it's just part of the growing pains. The web is successful because it's easy to layer businesses on top of each other... I can have a Tumblr with a Shopify backend and Google Adwords on top. Apps are walled gardens so they can only enforce one business model at a time. That can make things nice and tidy, but it walls you out of the messy, compositional business models of the web.

Because business models are composed on the web, it's just harder to settle on unified design standards. It takes time for everyone to agree on a separation of responsibilities on the page. This is compounded by the sheer newness of the business models. My webcomic about fancy cheeses has a segment marketing a line of tractors now to industrial buyers at a conference in Wisconsin this week? OK. That's an opportunity I probably wouldn't have had selling Java apps.