The dilemma for developers: Should they create innovative native apps that take advantage of the unique features of a particular handset, such as the iPhone’s accelerometer, or produce more basic apps that will run across many different handsets?

That might seem like a no-brainer given the collective failure of handset manufacturers to implement a standard Java run time environment, the fragmentation of Web run time platforms and the high sales levels achieved by some native apps for the iPhone. “Supporting Java on some phones is like sticking forks in your legs,” Sean O’ Sullivan of Dial2Do told the recent Mobile Web 2.0 summit. “Native apps are how you get the optimal user experience.”

“Many apps have been developed to work on the lowest common denominator,” added Ilja Laurs of independent app store GetJar, which now intends to rank apps by market and device rather than across all devices and all markets. “That should lead to a significant increase in product quality because the developers won’t be so motivated to spread themselves across so many devices,” Laurs told the event.

But do developers really want to bet on a small number of handsets? Laurs himself estimated that developers typically need to sell 10,000 copies of an app just to cover their costs and, in highly-competitive app stores, achieving that level of sales across a handful of devices isn’t easy.

For mobile operators, the fragmentation created by native apps is also a headache. Wim de Mooij of Orange called on the mobile industry to standardise Web run time environments in the same way it standardised GSM to create economies of scale for developers and operators.

In the struggle between standardisation and differentiation, which force will win out?