By forcing Web developers, and ultimately Adobe, out of the Flash business, Apple made HTML5 apps better. That’s good for Safari users, but it’s also good for users on other Web platforms, like Android. If there’s a truly good universal platform for online apps, it stands to reason that the smart developer will build apps for it, since this way the app will be available to the largest number of users. Right?

Furthermore, now that Adobe has HTML5 religion, the company is releasing high-quality HTML5 developer tools, migrating its Flash developers over to the new platform. So we should be about to see a flood of new Web-based mobile apps.

All this appears to be just as Apple intended: Steve Jobs’ campaign to rid the world of Flash is succeeding. The Web is getting better apps and the Web-browsing experience on Apple’s mobile devices is getting better.

But this could be bad news for Apple’s lucrative App Store business. While Apple takes a 30 percent cut of all app sales through its store (still the only way for consumers to get apps), Apple gets 0 percent of “Web apps” loaded up through the browser. The better HTML5 gets, the less developers will write apps, less money Apple will make, and the less unique the iPhone and iPad will be.

I talked with the CEO of a Web company who is excited about the advances in HTML5 because he sees a future in which the devices and operating systems are on the same level. It’s a world where new products, like Microsoft Windows phones, can come along and be instantly competitive. And where companies like his can have a shot at dominance in their market niche after building only one app, the HTML5 version.

In other words, Apple, in pushing the world toward HTML5, is killing its own golden goose.

Or is it?

The counter argument comes from another CEO, one who’s built a successful business around both Web services, and software for mobiles and traditional computers. He says that apps are here to stay, because the “lowest common denominator” strategy (using the Web) doesn’t cut it for developers ultimately, nor for consumers, and most importantly not for the tech megaliths behind mobile operating systems: Apple, Google, and Microsoft.

The challenge for apps developers, my source explains, is getting their apps seen for more than a fleeting moment. For those making Web apps, there’s just no good way. Even a good review of a Web app on a popular site has only a temporary impact. The way to get your app in front of potential customers, time and again, is to get it featured in an app store.

You do that by building an app that highlights its unique hardware capabilities–the features that the hardware company is using to sell the product. These will likely be features that you can’t access today, or in the foreseeable future, with a Web app. This isn’t because HTML5 won’t advance, but because the device and OS manufacturers will always do their best to keep their products somewhat ahead of the lower-common-denominator Web platform. It is how they sell products.

So if you make a mobile app, you want to feed into that trend, because it will feed you.

And what about HTML5? It’s good for apps that don’t depend on the app stores for sales. The means enterprise apps, essentially. HTML5 has its place in consumer apps, too, including inside many successful mobile apps. But not for the core features or the main UI.

Relying on HTML5 to quickly get to broad compatibility across the mobile landscape is a trap, my guy says. To succeed, you need to tackle each platform separately. In fact, he says, you might want to build apps that only work on the latest and greatest version of a phone, and intentionally not on previous models. Yes, fewer people will be able to use it. But everyone who buys the new toy will. The more your app makes the hot new hardware look good, the more it’ll get promoted by the hardware or OS manufacturer. That can give your app presence it could not otherwise get. Once your product is succeeding on the brand-new hardware, you can start adapting it to other platforms.

Try to conquer the entire mobile world at once and you’ll have no marketing partners. Or, put more starkly: It’s hard to win when nobody loses.a