The same way you did before there was an app store - through your website. As for Android, you can sell APKs through your site that people can sideload onto their phones.
People already complain about too much competition on the App store. On the web you're competing with virus' and everything else as well. And people have to figure out where you are.
Having your app on the App store is like having it in some giant big box store. Having it on the web is like having your app somewhere on the planet.
How does it work? Do you just send ipa files that the user is expected to import into itunes?
Apple has been treating their developers like crap ever since the app store opened, and the only way to change it is to vote with your wallet (or more accurately in this case, your development time). Otherwise, you are part of the problem.