Knowing that option exists and persisting with their store-only approach means they must have an ulterior motive of some sort, most likely control and money. Ad blockers that target Google Ads will be no more, as well as anything else that the user might want to use to subvert or circumvent. Extensions will also have to adhere to Google's moral code, and developers will once again be beholden to a greater authority in order to operate their business.
Just like with Facebook and the Apple app store, if you build a business on Google Chrome Extensions you now face having the plug pulled at any time for any reason, with absolutely no recourse.
[1] http://blog.chromium.org/2013/11/protecting-windows-users-fr...