From a consumer perspective, software prices in real terms have gone down dramatically since those days. Apple brought unprecedented scale and discovery to a software marketplace, and consumers have benefitted.
There's also no choice with Best Buy. If you walk into a Best Buy, you pay Best Buy prices.
If you don't want to pay iOS prices, you go to Android. If you don't want to go to Android, you can go try and find a Firefox OS phone, or a Ubuntu one.
The problem isn't that choice doesn't exist. The problem is that equivalent choices don't exist.
Bestbuy doesn't charge you hundreds of dollars to buy the store before you walk in.
Consumers don't own Bestbuy, Bestbuy owns Bestbuy, so it's okay for Bestbuy to control the shelf space in their own stores.
It is not okay for Bestbuy to exclusively own the app shelfspace on your own phone. Just as it is not okay for Bestbuy to exclusively charge a premium to it's competition when you, the user, are signing up for services with the competition on your own phone.
Does Costco sell things at a markup? They are famous for having net income equal to the amount of membership fees they collect, so they must be selling products at however much it costs to obtain the products and operate the stores.
You aren't buying the Costco store when you enter, just as you aren't paying a membership fee to use someone else's phone as your own.
Members don't own Costco, Costco owns Costco, so Costco can dictate it's own shelfspace. You would not expect Costco to exclusively dictate what apps you can and cannot buy on your own phone or charge a premium to Costco competition.
We used to actually buy software in stores. Developers used to have give CompUSA, and Best Buy, etc. massive cuts just to be on their shelves.