I don't understand why they did it with Skyrim.
I do. They knew there'd be controversy, so they're springing it early and letting it happen now with an older, well-modded game so that when the next game* hits the paid mod system's already in place and the wailing/gnashing of teeth has long subsided.
spoiler (click to show/hide)
*Fallout 4's coming this holiday (or early, early next year). As soon as Bethesda announced their E3 conference/presentation/whatever I knew it would be. I know a lot of people don't think it will, but Dishonored isn't a big enough game to build a conference around (sorry, Dishonored fans). I don't really think Doom holds that kind of cache anymore, either. I doubt they'd spend the money to put together a staged media presentation for a FO4 that's a year (or even two) out, when they could save the cash and do that by riding along with MS/Sony during those conferences. I'd be willing to bet the big drop is FO4 for this year (or again, very early next year). And you'll be paying for those mods right out of the gate!