John Gruber points to Brent Simmons’ nuanced take on Dave Winer’s much-discussed assertion that native (mobile) apps are not the future and the web will take over. I’ve written often about the “war” between native apps and the web (or web apps, if you prefer) and the most interesting conclusion about what the future holds – whether it’s open, like the web, or closed, like Apple’s app store – has always been that the future holds both.

Simmons goes further, however, and asserts that because the server-side architecture that all apps rely on, both native and web, is now so clean and discrete and independent of its presentation on a phone by a website or an app, the future is actually web apps and native apps that are basically indistinguishable.

I think instead that we’ll see a more tangled future. Native apps will use HTML, CSS, and JavaScript more. Web apps will appear more often on smart phones as launchable apps. Native apps will support linking in and out more. Web apps will move more processing to the client — they’ll be written more like native apps. (Is Twitter an app or a web app? It’s already getting tangled.)

I’ve covered examples of hybrid native apps before, but Simmons raises two possibilities that are barely supported in today’s mobile OSes. The intriguing possibility is that both will come to pass:

1. More cross-linking abilities in apps.

The reason that Winer says the web will always “win” is that websites link to one another. It’s impossible, at present, to link to a particular page or state within an app. But there’s no reason this couldn’t work in the future, as long as you have an app pre-installed. Granted, that’s a high energy barrier for most of us, but if it were a popular app, why not? After all, Linden Labs was linking to locations in Second Life long before the iPhone was twinkle in Steve Jobs’s eye.

2. True cross-platform support for web apps.

Smartphones already support bookmarks to web apps that look just like native apps, but on the iPhone, at least, this functionality isn’t nearly as obvious as the app store itself. In addition, differences between HTML5 support on phones are significant enough that web apps like those built by Financial Times had to be built twice – once for iOS, a second time for Android – despite the cross-platform promise of HTML5.