It's wrong to compare iPhones, iPads, iWhatevers to gaming consoles at this time.
Any of those devices is made for the sole purpose of running games which software houses make for it. Nothing more.
Every console has a rigid software platform, and online games are played only through the console producer's network. You know it when you buy the console, you know it when you produce a game for it.
That's how the console market works and that's well known and accepted by console producers, game producers, and users.
Smartphones do surf the web. The web is full of standards, some open and some closed, and on those standards with corresponding API layers there are lots of software houses and other companies that run their businesses.
Since applications and services running on the web are distributed applications, devices accessing the web run the client side of those applications, and should be able of running software that respects the actually common standards on the web.
That's how the PC and smartphones market works and that's well known and accepted by users, hardware producers and software producers: except for Apple it seems.
Ruling which of these technologies should be banned from the user devices means influencing businesses of companies that supply services through the web and means influencing choices users can make (i.e. choosing an online web service or another), so it means influencing the market.
We are not talking about a standard that isn't implemented on Apple's platform: indeed, Flash support is ready. Remember that Microsoft, that just makes software, had been ruled by the EU antitrust to show users a choice screen for browsers, just to be sure that browser other than Internet Explorer do exist.
Apple makes the hardware AND the software, forces consumers to buy hardware with their brand if they want to use Apple software, and now wants to decide that users can't use web services made with a concurrent technology. It's a bit more restricting and destructive compared to MS practices: it's quite normal an inquiry started.
Of course if iPhones were sold as gaming consoles it would be a lot easy for Apple to justify. But they aren't: they are sold as smartphones.