In my opinion, Microsoft still appears to be saying that Linked Servers are a viable and recommended option to integrate one SQL instance to another. In practice, Linked Servers tend to introduce system failures and tight coupling of systems. e.g. If one SQL instance goes down, the other will rollback transactions. I don't think most applications are prepared to handle this problem. MSDTC also introduces another failure point. Linked Servers also tend to have performance problems, due to inexperienced developers issuing JOINs between two instance. That is SQL Server often does not create efficient query plans for a query like: select ... from myServerA.myDb.dbo.myTable JOIN myServerB.myOtherDb.dbo.myOther Table etc. As these are two different SQL instances. In short, Linked Servers create a low performing, tightly coupled integration with more failure points: network, DTC, and the other SQL instance.
Linked servers: permissions and distributed query performance