OK, Apple (NASDAQ:AAPL) isn't the new Big Brother. But the real Big Brother is asking Apple what the heck it's up to.

A briskly worded letter sent by FCC bureau chief James Schlichting asks Apple to explain why the company rejected an official Google (NASDAQ:GOOG) Voice application and removed several unofficial third-party apps from its iPhone app store. Among the questions asked, a couple caught my eye:

  • Did Apple "act alone or in consultation with" exclusive U.S. iPhone service provider AT&T (NYSE:T)?
  • "Please explain any differences" between the rejected apps and any other voice over Internet (VoIP) applications that remain in the store.
  • "What are the standards for considering and approving iPhone applications?"

When Apple distanced itself from all the Google Voice apps, the company may have lost a few customers. That includes high-profile TechCrunch founder Michael Arrington, who says he'd rather take the $175 termination fee and switch to a Google-backed Android phone than worry about the whims of Apple's store policies.

"It's not an easy decision," says Arrington. "Except, it sort of is. Google isn't forcing the decision on me, Apple and AT&T are. So I choose to work with the company that isn't forcing me to do things their way."

The queries seem to paint Apple's approval processes as opaque and possibly unreasonable. Did AT&T have a finger in this debacle? I think it likely, but don't forget that Ma Bell is far from Apple's only partner. Vodafone (NYSE:VOD) sells the iPhone in markets like India and Italy, for example, and Deutsche Telekom (NYSE:DT) subsidiary T-Mobile handles several European markets, including the Netherlands and Austria.

More than 20 different operators have iPhone distribution deals. AT&T can't be the only one worrying about its own highly profitable services being made obsolete by Google Voice.

Today, Google has official Google Voice apps for the Android and for Research In Motion (NASDAQ:RIMM) BlackBerry phones. The Palm (NASDAQ:PALM) Pre may be a worthy replacement for the iPhone in many ways -- but it, too, lacks an official Google Voice application at this time.

Would you eat a termination fee to preserve your right to choose software applications? I'm in the process of choosing a new smartphone myself, and let's just say Apple didn't exactly win my business with this fiasco. Lather, rinse, and repeat -- and the defections could add up to serious amounts of lost business.

Further Foolishness:

Start investing today -- just $7 per trade with Scottrade. Or find the broker that's right for you.

Google is a Motley Fool Rule Breakers pick. Apple is a Motley Fool Stock Advisor recommendation. Try any of our Foolish newsletters today, free for 30 days.

Fool contributor Anders Bylund owns shares in Google, but he holds no other position in any of the companies discussed here. You can check out Anders' holdings or a concise bio if you like, and The Motley Fool is investors writing for investors.