OmniGroup found a way to effectively get upgrade pricing with the App Store, but it requires your app have two modes: Regular mode, and an in-app purchase to Pro mode. With that setup, you can offer discounts for the IAP to previous customers (basically, by having 2 IAPs that unlock the same functionality, but you only present one to the user). So your repeat customers still need to pay full price for the Regular edition but their Pro upgrade is cheap (or free).
Of course, most apps don't really split into Regular and Pro very well, so this solution won't work for a lot of people.
That's pretty bad way to alienate your loyal customers. They can still have users email them and issue download codes after paying through their website.
No they can't. The App Store very deliberately prevents that (because that would let you use the App Store for all its benefits, while completely bypassing the 30% cut). The only codes you get are a limited number of promotional codes. Sure, if you have 5 customers, you could give them codes, but if you have 500 you can't.
the last one is rarely used by Developers… 1Password is one, that allows you to buy it in the MAS, and use at least their Beta-Builds.
That many developers use the MAS as an excuse, for not providing any upgrade paths at all… is a very silly solution to a problem that many Developers/Companys face (to make permanent profit) at the cost of customer satisfaction.