I work on a on-going project for past two years, which has thousands of files. I cannot enable the Code Analysis only for the new development. In other words, i cannot go class by class to suppress the Code Analyses. FxCop allows us to select the classes for which we need to have code analysis run. That may be the only dis-advantage with the integrated Code Analysis Tool. Hope this is facilitated in the new versions of Code Analysis Tool.
Otherwise, it helps us during coding and compile time, where FxCop, will help only after compile time.