Not having retweets in the user_timeline represents a loss of functionality.
With user_timeline you can get the tweets of any user using the "id" parameter, but there is no way to get the tweets of another user using home_timeline without being authenticated *as that user*. So this limits the ability of applications to gather info for a user without requiring them to log in. Before the retweet funcdtionality was added, "organic" retweets were of course visible. The built-in retweets are not.